Starting phenix.real_space_refine on Wed Feb 21 11:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wrc_32722/02_2024/7wrc_32722_updated.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 140 5.16 5 C 19820 2.51 5 N 5052 2.21 5 O 5452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ARG 784": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 842": "NH1" <-> "NH2" Residue "A ARG 851": "NH1" <-> "NH2" Residue "A ARG 885": "NH1" <-> "NH2" Residue "A PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 119": "NH1" <-> "NH2" Residue "B ARG 784": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 842": "NH1" <-> "NH2" Residue "B ARG 851": "NH1" <-> "NH2" Residue "B ARG 885": "NH1" <-> "NH2" Residue "B PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 119": "NH1" <-> "NH2" Residue "C ARG 784": "NH1" <-> "NH2" Residue "C ARG 816": "NH1" <-> "NH2" Residue "C ARG 842": "NH1" <-> "NH2" Residue "C ARG 851": "NH1" <-> "NH2" Residue "C ARG 885": "NH1" <-> "NH2" Residue "C PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 119": "NH1" <-> "NH2" Residue "D ARG 784": "NH1" <-> "NH2" Residue "D ARG 816": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 851": "NH1" <-> "NH2" Residue "D ARG 885": "NH1" <-> "NH2" Residue "D PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30468 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "B" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "C" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "D" Number of atoms: 7593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7593 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 23, 'TRANS': 906} Chain breaks: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' CA': 1, 'KX7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.83, per 1000 atoms: 0.55 Number of scatterers: 30468 At special positions: 0 Unit cell: (155.142, 155.142, 157.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 140 16.00 O 5452 8.00 N 5052 7.00 C 19820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 929 " - pdb=" SG CYS A 940 " distance=2.01 Simple disulfide: pdb=" SG CYS B 929 " - pdb=" SG CYS B 940 " distance=2.01 Simple disulfide: pdb=" SG CYS C 929 " - pdb=" SG CYS C 940 " distance=2.01 Simple disulfide: pdb=" SG CYS D 929 " - pdb=" SG CYS D 940 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.16 Conformation dependent library (CDL) restraints added in 5.6 seconds 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 4 sheets defined 61.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'A' and resid 126 through 135 Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 188 through 203 removed outlier: 3.726A pdb=" N ARG A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 Processing helix chain 'A' and resid 310 through 321 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 351 through 361 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 384 removed outlier: 4.169A pdb=" N SER A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.711A pdb=" N TYR A 410 " --> pdb=" O ASN A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 459 through 467 Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 484 through 487 No H-bonds generated for 'chain 'A' and resid 484 through 487' Processing helix chain 'A' and resid 490 through 498 Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.621A pdb=" N ARG A 507 " --> pdb=" O THR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 531 Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 587 through 603 removed outlier: 4.239A pdb=" N LYS A 603 " --> pdb=" O LYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 635 removed outlier: 3.621A pdb=" N GLU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 removed outlier: 4.279A pdb=" N VAL A 645 " --> pdb=" O GLU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 662 Processing helix chain 'A' and resid 672 through 683 Processing helix chain 'A' and resid 692 through 700 Processing helix chain 'A' and resid 702 through 705 removed outlier: 3.748A pdb=" N VAL A 705 " --> pdb=" O ILE A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 734 through 758 Processing helix chain 'A' and resid 766 through 789 Processing helix chain 'A' and resid 792 through 795 Processing helix chain 'A' and resid 797 through 816 Processing helix chain 'A' and resid 822 through 849 removed outlier: 4.269A pdb=" N LEU A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 removed outlier: 3.595A pdb=" N GLN A 861 " --> pdb=" O ILE A 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 889 Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.064A pdb=" N SER A 902 " --> pdb=" O TRP A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 911 removed outlier: 4.099A pdb=" N MET A 911 " --> pdb=" O PRO A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 953 through 968 Proline residue: A 958 - end of helix Processing helix chain 'A' and resid 970 through 986 removed outlier: 3.602A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 990 through 1006 removed outlier: 4.434A pdb=" N TYR A 999 " --> pdb=" O LYS A 995 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE A1000 " --> pdb=" O PHE A 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1029 removed outlier: 4.015A pdb=" N VAL A1017 " --> pdb=" O PRO A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1070 removed outlier: 3.862A pdb=" N VAL A1058 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A1059 " --> pdb=" O TRP A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1103 Processing helix chain 'B' and resid 126 through 135 Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.726A pdb=" N ARG B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 286 Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.169A pdb=" N SER B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 417 removed outlier: 3.712A pdb=" N TYR B 410 " --> pdb=" O ASN B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 439 through 445 Processing helix chain 'B' and resid 459 through 467 Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 484 through 487 No H-bonds generated for 'chain 'B' and resid 484 through 487' Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'B' and resid 503 through 515 removed outlier: 3.621A pdb=" N ARG B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 531 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 576 through 581 Processing helix chain 'B' and resid 587 through 603 removed outlier: 4.239A pdb=" N LYS B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 635 removed outlier: 3.620A pdb=" N GLU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 4.278A pdb=" N VAL B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 672 through 683 Processing helix chain 'B' and resid 692 through 700 Processing helix chain 'B' and resid 702 through 705 removed outlier: 3.748A pdb=" N VAL B 705 " --> pdb=" O ILE B 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 702 through 705' Processing helix chain 'B' and resid 724 through 731 Processing helix chain 'B' and resid 734 through 758 Processing helix chain 'B' and resid 766 through 789 Processing helix chain 'B' and resid 792 through 795 Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 822 through 849 removed outlier: 4.270A pdb=" N LEU B 843 " --> pdb=" O PHE B 839 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE B 844 " --> pdb=" O THR B 840 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 862 removed outlier: 3.595A pdb=" N GLN B 861 " --> pdb=" O ILE B 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 862 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 889 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.063A pdb=" N SER B 902 " --> pdb=" O TRP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 911 removed outlier: 4.098A pdb=" N MET B 911 " --> pdb=" O PRO B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 928 No H-bonds generated for 'chain 'B' and resid 926 through 928' Processing helix chain 'B' and resid 953 through 968 Proline residue: B 958 - end of helix Processing helix chain 'B' and resid 970 through 986 removed outlier: 3.602A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1006 removed outlier: 4.434A pdb=" N TYR B 999 " --> pdb=" O LYS B 995 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B1001 " --> pdb=" O GLN B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1029 removed outlier: 3.996A pdb=" N VAL B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1047 through 1070 removed outlier: 3.861A pdb=" N VAL B1058 " --> pdb=" O ALA B1054 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B1059 " --> pdb=" O TRP B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1103 Processing helix chain 'C' and resid 126 through 135 Processing helix chain 'C' and resid 159 through 175 Processing helix chain 'C' and resid 188 through 203 removed outlier: 3.726A pdb=" N ARG C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 286 Processing helix chain 'C' and resid 310 through 321 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 351 through 361 Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 371 through 384 removed outlier: 4.169A pdb=" N SER C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 417 removed outlier: 3.711A pdb=" N TYR C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 459 through 467 Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 484 through 487 No H-bonds generated for 'chain 'C' and resid 484 through 487' Processing helix chain 'C' and resid 490 through 498 Processing helix chain 'C' and resid 503 through 515 removed outlier: 3.621A pdb=" N ARG C 507 " --> pdb=" O THR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 531 Processing helix chain 'C' and resid 560 through 570 Processing helix chain 'C' and resid 576 through 581 Processing helix chain 'C' and resid 587 through 603 removed outlier: 4.240A pdb=" N LYS C 603 " --> pdb=" O LYS C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 635 removed outlier: 3.620A pdb=" N GLU C 631 " --> pdb=" O GLU C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 removed outlier: 4.279A pdb=" N VAL C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 662 Processing helix chain 'C' and resid 672 through 683 Processing helix chain 'C' and resid 692 through 700 Processing helix chain 'C' and resid 702 through 705 removed outlier: 3.748A pdb=" N VAL C 705 " --> pdb=" O ILE C 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 702 through 705' Processing helix chain 'C' and resid 724 through 731 Processing helix chain 'C' and resid 734 through 758 Processing helix chain 'C' and resid 766 through 789 Processing helix chain 'C' and resid 792 through 795 Processing helix chain 'C' and resid 797 through 816 Processing helix chain 'C' and resid 822 through 849 removed outlier: 4.269A pdb=" N LEU C 843 " --> pdb=" O PHE C 839 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 844 " --> pdb=" O THR C 840 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS C 845 " --> pdb=" O LEU C 841 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 848 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 862 removed outlier: 3.595A pdb=" N GLN C 861 " --> pdb=" O ILE C 857 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG C 862 " --> pdb=" O ILE C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 889 Processing helix chain 'C' and resid 896 through 903 removed outlier: 4.064A pdb=" N SER C 902 " --> pdb=" O TRP C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 911 removed outlier: 4.099A pdb=" N MET C 911 " --> pdb=" O PRO C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 926 through 928 No H-bonds generated for 'chain 'C' and resid 926 through 928' Processing helix chain 'C' and resid 953 through 968 Proline residue: C 958 - end of helix Processing helix chain 'C' and resid 970 through 986 removed outlier: 3.602A pdb=" N LEU C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1006 removed outlier: 4.433A pdb=" N TYR C 999 " --> pdb=" O LYS C 995 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE C1000 " --> pdb=" O PHE C 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU C1001 " --> pdb=" O GLN C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1014 through 1029 removed outlier: 3.985A pdb=" N VAL C1017 " --> pdb=" O PRO C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1047 through 1070 removed outlier: 3.862A pdb=" N VAL C1058 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C1059 " --> pdb=" O TRP C1055 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1103 Processing helix chain 'D' and resid 126 through 135 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 203 removed outlier: 3.725A pdb=" N ARG D 203 " --> pdb=" O ASN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 286 Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 351 through 361 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 371 through 384 removed outlier: 4.169A pdb=" N SER D 376 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 417 removed outlier: 3.711A pdb=" N TYR D 410 " --> pdb=" O ASN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 435 Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 459 through 467 Processing helix chain 'D' and resid 471 through 479 Processing helix chain 'D' and resid 484 through 487 No H-bonds generated for 'chain 'D' and resid 484 through 487' Processing helix chain 'D' and resid 490 through 498 Processing helix chain 'D' and resid 503 through 515 removed outlier: 3.621A pdb=" N ARG D 507 " --> pdb=" O THR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 531 Processing helix chain 'D' and resid 560 through 570 Processing helix chain 'D' and resid 576 through 581 Processing helix chain 'D' and resid 587 through 603 removed outlier: 4.239A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 635 removed outlier: 3.619A pdb=" N GLU D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 removed outlier: 4.279A pdb=" N VAL D 645 " --> pdb=" O GLU D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 662 Processing helix chain 'D' and resid 672 through 683 Processing helix chain 'D' and resid 692 through 700 Processing helix chain 'D' and resid 702 through 705 removed outlier: 3.748A pdb=" N VAL D 705 " --> pdb=" O ILE D 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 702 through 705' Processing helix chain 'D' and resid 724 through 731 Processing helix chain 'D' and resid 734 through 758 Processing helix chain 'D' and resid 766 through 789 Processing helix chain 'D' and resid 792 through 795 Processing helix chain 'D' and resid 797 through 816 Processing helix chain 'D' and resid 822 through 849 removed outlier: 4.269A pdb=" N LEU D 843 " --> pdb=" O PHE D 839 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE D 844 " --> pdb=" O THR D 840 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N HIS D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 848 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 862 removed outlier: 3.595A pdb=" N GLN D 861 " --> pdb=" O ILE D 857 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG D 862 " --> pdb=" O ILE D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 889 Processing helix chain 'D' and resid 896 through 903 removed outlier: 4.064A pdb=" N SER D 902 " --> pdb=" O TRP D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 905 through 911 removed outlier: 4.098A pdb=" N MET D 911 " --> pdb=" O PRO D 907 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 928 No H-bonds generated for 'chain 'D' and resid 926 through 928' Processing helix chain 'D' and resid 953 through 968 Proline residue: D 958 - end of helix Processing helix chain 'D' and resid 970 through 986 removed outlier: 3.602A pdb=" N LEU D 975 " --> pdb=" O LEU D 971 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1006 removed outlier: 4.434A pdb=" N TYR D 999 " --> pdb=" O LYS D 995 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE D1000 " --> pdb=" O PHE D 996 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU D1001 " --> pdb=" O GLN D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1014 through 1029 removed outlier: 4.014A pdb=" N VAL D1017 " --> pdb=" O PRO D1014 " (cutoff:3.500A) Processing helix chain 'D' and resid 1047 through 1070 removed outlier: 3.861A pdb=" N VAL D1058 " --> pdb=" O ALA D1054 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET D1059 " --> pdb=" O TRP D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1075 through 1103 Processing sheet with id= A, first strand: chain 'A' and resid 119 through 121 removed outlier: 7.893A pdb=" N LEU A 120 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU A 262 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 119 through 121 removed outlier: 7.893A pdb=" N LEU B 120 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 262 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 119 through 121 removed outlier: 7.892A pdb=" N LEU C 120 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU C 262 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 119 through 121 removed outlier: 7.893A pdb=" N LEU D 120 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU D 262 " --> pdb=" O LEU D 120 " (cutoff:3.500A) 1588 hydrogen bonds defined for protein. 4596 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: 10.83 Time building geometry restraints manager: 13.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4884 1.30 - 1.43: 8745 1.43 - 1.56: 17347 1.56 - 1.69: 0 1.69 - 1.82: 212 Bond restraints: 31188 Sorted by residual: bond pdb=" N21 KX7 D1202 " pdb=" O23 KX7 D1202 " ideal model delta sigma weight residual 1.208 1.399 -0.191 2.00e-02 2.50e+03 9.08e+01 bond pdb=" N21 KX7 A1202 " pdb=" O23 KX7 A1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" N21 KX7 B1202 " pdb=" O23 KX7 B1202 " ideal model delta sigma weight residual 1.208 1.398 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" N21 KX7 C1202 " pdb=" O23 KX7 C1202 " ideal model delta sigma weight residual 1.208 1.397 -0.189 2.00e-02 2.50e+03 8.96e+01 bond pdb=" C05 KX7 C1202 " pdb=" N07 KX7 C1202 " ideal model delta sigma weight residual 1.355 1.482 -0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 31183 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.46: 222 103.46 - 111.15: 11485 111.15 - 118.83: 13489 118.83 - 126.51: 16508 126.51 - 134.20: 548 Bond angle restraints: 42252 Sorted by residual: angle pdb=" N PHE D1013 " pdb=" CA PHE D1013 " pdb=" C PHE D1013 " ideal model delta sigma weight residual 113.16 121.60 -8.44 1.42e+00 4.96e-01 3.53e+01 angle pdb=" N PHE C1013 " pdb=" CA PHE C1013 " pdb=" C PHE C1013 " ideal model delta sigma weight residual 113.16 121.29 -8.13 1.42e+00 4.96e-01 3.28e+01 angle pdb=" N PHE A1013 " pdb=" CA PHE A1013 " pdb=" C PHE A1013 " ideal model delta sigma weight residual 113.16 121.23 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" N PHE B1013 " pdb=" CA PHE B1013 " pdb=" C PHE B1013 " ideal model delta sigma weight residual 113.16 121.17 -8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" N ASN B1010 " pdb=" CA ASN B1010 " pdb=" C ASN B1010 " ideal model delta sigma weight residual 109.24 117.84 -8.60 1.63e+00 3.76e-01 2.78e+01 ... (remaining 42247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 17136 15.20 - 30.41: 908 30.41 - 45.61: 216 45.61 - 60.82: 12 60.82 - 76.02: 32 Dihedral angle restraints: 18304 sinusoidal: 7392 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ILE B 985 " pdb=" C ILE B 985 " pdb=" N VAL B 986 " pdb=" CA VAL B 986 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE A 985 " pdb=" C ILE A 985 " pdb=" N VAL A 986 " pdb=" CA VAL A 986 " ideal model delta harmonic sigma weight residual 180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE D 985 " pdb=" C ILE D 985 " pdb=" N VAL D 986 " pdb=" CA VAL D 986 " ideal model delta harmonic sigma weight residual -180.00 -154.31 -25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 18301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3442 0.064 - 0.127: 1078 0.127 - 0.191: 167 0.191 - 0.255: 17 0.255 - 0.318: 4 Chirality restraints: 4708 Sorted by residual: chirality pdb=" CA PHE D1013 " pdb=" N PHE D1013 " pdb=" C PHE D1013 " pdb=" CB PHE D1013 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA PHE A1013 " pdb=" N PHE A1013 " pdb=" C PHE A1013 " pdb=" CB PHE A1013 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PHE C1013 " pdb=" N PHE C1013 " pdb=" C PHE C1013 " pdb=" CB PHE C1013 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 4705 not shown) Planarity restraints: 5280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C1011 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ILE C1011 " -0.076 2.00e-02 2.50e+03 pdb=" O ILE C1011 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO C1012 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1011 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C ILE A1011 " -0.075 2.00e-02 2.50e+03 pdb=" O ILE A1011 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A1012 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D1011 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ILE D1011 " -0.074 2.00e-02 2.50e+03 pdb=" O ILE D1011 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO D1012 " 0.025 2.00e-02 2.50e+03 ... (remaining 5277 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6067 2.77 - 3.30: 28889 3.30 - 3.83: 49095 3.83 - 4.37: 58250 4.37 - 4.90: 98175 Nonbonded interactions: 240476 Sorted by model distance: nonbonded pdb=" O ILE A 888 " pdb=" OH TYR B 826 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 205 " pdb=" OE1 GLU A 206 " model vdw 2.262 2.440 nonbonded pdb=" OG SER C 205 " pdb=" OE1 GLU C 206 " model vdw 2.262 2.440 nonbonded pdb=" OG SER B 205 " pdb=" OE1 GLU B 206 " model vdw 2.262 2.440 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 206 " model vdw 2.263 2.440 ... (remaining 240471 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.800 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: 5.160 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 80.700 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.010 0.191 31188 Z= 0.638 Angle : 1.068 9.619 42252 Z= 0.592 Chirality : 0.060 0.318 4708 Planarity : 0.007 0.064 5280 Dihedral : 10.593 76.021 11212 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.12 % Allowed : 2.82 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.11), residues: 3656 helix: -2.12 (0.08), residues: 2436 sheet: -1.76 (0.32), residues: 200 loop : -3.48 (0.15), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRP B 377 HIS 0.008 0.002 HIS D 185 PHE 0.030 0.003 PHE C 832 TYR 0.040 0.004 TYR D1005 ARG 0.007 0.001 ARG B 688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 802 time to evaluate : 3.427 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: A 256 ASN cc_start: 0.8449 (m-40) cc_final: 0.8055 (m-40) REVERT: A 306 GLN cc_start: 0.7191 (pp30) cc_final: 0.6667 (tm-30) REVERT: A 330 GLU cc_start: 0.8627 (mp0) cc_final: 0.8330 (mp0) REVERT: A 661 VAL cc_start: 0.9268 (t) cc_final: 0.9039 (p) REVERT: A 723 LEU cc_start: 0.7606 (mm) cc_final: 0.7294 (tt) REVERT: A 859 MET cc_start: 0.8255 (ttp) cc_final: 0.7377 (ttm) REVERT: A 928 HIS cc_start: 0.7720 (m90) cc_final: 0.7440 (m-70) REVERT: B 723 LEU cc_start: 0.7920 (mm) cc_final: 0.7717 (tt) REVERT: B 860 LEU cc_start: 0.9155 (tp) cc_final: 0.8955 (tp) REVERT: B 1023 MET cc_start: 0.5629 (mmm) cc_final: 0.5273 (mmm) REVERT: C 201 ILE cc_start: 0.8316 (tp) cc_final: 0.6637 (tp) REVERT: C 325 PRO cc_start: 0.7693 (Cg_endo) cc_final: 0.7437 (Cg_exo) REVERT: C 723 LEU cc_start: 0.7960 (mm) cc_final: 0.7720 (tt) REVERT: D 146 ILE cc_start: 0.7497 (mt) cc_final: 0.7246 (mt) REVERT: D 252 ILE cc_start: 0.7907 (mm) cc_final: 0.7704 (mm) REVERT: D 325 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: D 1023 MET cc_start: 0.5654 (mmm) cc_final: 0.5356 (mmm) outliers start: 4 outliers final: 0 residues processed: 802 average time/residue: 0.4581 time to fit residues: 570.3606 Evaluate side-chains 463 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 291 optimal weight: 30.0000 chunk 112 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 337 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 173 GLN ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 HIS A 270 HIS A 279 ASN A 483 ASN A 671 GLN A1102 ASN B 136 HIS B 204 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 HIS B 483 ASN B 572 ASN B 671 GLN B 675 GLN C 136 HIS C 204 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS C 438 GLN C 989 ASN C1102 ASN D 136 HIS D 204 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS D 294 ASN D 438 GLN D 483 ASN D 671 GLN D 789 ASN D 973 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31188 Z= 0.192 Angle : 0.623 7.675 42252 Z= 0.325 Chirality : 0.040 0.181 4708 Planarity : 0.005 0.117 5280 Dihedral : 5.940 47.177 4024 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.01 % Allowed : 9.95 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3656 helix: -0.36 (0.10), residues: 2436 sheet: -1.80 (0.32), residues: 188 loop : -2.95 (0.16), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 898 HIS 0.005 0.001 HIS C 138 PHE 0.016 0.001 PHE C 809 TYR 0.016 0.001 TYR D 787 ARG 0.005 0.000 ARG D1081 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 517 time to evaluate : 3.824 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: A 201 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 306 GLN cc_start: 0.7272 (pp30) cc_final: 0.6840 (tm-30) REVERT: A 353 MET cc_start: 0.7865 (mpp) cc_final: 0.7622 (pmm) REVERT: A 723 LEU cc_start: 0.7746 (mm) cc_final: 0.7480 (tt) REVERT: A 801 MET cc_start: 0.7974 (ppp) cc_final: 0.7717 (ptm) REVERT: B 201 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8097 (tp) REVERT: B 364 ARG cc_start: 0.8089 (mtm180) cc_final: 0.7859 (tmt170) REVERT: B 860 LEU cc_start: 0.9096 (tp) cc_final: 0.8883 (tp) REVERT: B 918 ASP cc_start: 0.7870 (p0) cc_final: 0.7640 (p0) REVERT: B 937 LYS cc_start: 0.7787 (mtmm) cc_final: 0.7501 (mtmm) REVERT: B 1023 MET cc_start: 0.5617 (mmm) cc_final: 0.5270 (mmm) REVERT: C 189 MET cc_start: 0.7888 (mpp) cc_final: 0.7448 (mpp) REVERT: C 325 PRO cc_start: 0.7726 (Cg_endo) cc_final: 0.7503 (Cg_exo) REVERT: C 364 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7753 (mtm180) REVERT: C 435 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 451 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6397 (ptt180) REVERT: C 801 MET cc_start: 0.7944 (ppp) cc_final: 0.7619 (ptp) REVERT: C 863 MET cc_start: 0.8322 (mmt) cc_final: 0.8039 (mmt) REVERT: D 189 MET cc_start: 0.7903 (mpp) cc_final: 0.7454 (mpp) REVERT: D 197 ARG cc_start: 0.8811 (ttp-110) cc_final: 0.8594 (ttp-110) REVERT: D 252 ILE cc_start: 0.8040 (mm) cc_final: 0.7627 (tt) REVERT: D 306 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6760 (tp-100) REVERT: D 435 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7531 (tm-30) REVERT: D 451 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.5690 (ptt-90) REVERT: D 789 ASN cc_start: 0.7813 (OUTLIER) cc_final: 0.7508 (t0) REVERT: D 863 MET cc_start: 0.8350 (mmt) cc_final: 0.8109 (mmt) REVERT: D 1013 PHE cc_start: 0.6614 (t80) cc_final: 0.6286 (t80) REVERT: D 1023 MET cc_start: 0.5731 (mmm) cc_final: 0.5435 (mmm) outliers start: 67 outliers final: 28 residues processed: 564 average time/residue: 0.4185 time to fit residues: 375.9670 Evaluate side-chains 466 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 433 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 985 ILE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 451 ARG Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 985 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 451 ARG Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 789 ASN Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1022 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 0.5980 chunk 301 optimal weight: 20.0000 chunk 335 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN A 419 ASN A 675 GLN A 765 HIS ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 419 ASN B 765 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN C 675 GLN C 765 HIS ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN D 294 ASN D 419 ASN D 675 GLN D 741 ASN D 765 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 31188 Z= 0.408 Angle : 0.735 11.981 42252 Z= 0.384 Chirality : 0.045 0.201 4708 Planarity : 0.005 0.100 5280 Dihedral : 5.782 49.708 4024 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.49 % Allowed : 11.87 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 3656 helix: 0.24 (0.10), residues: 2456 sheet: -1.83 (0.31), residues: 184 loop : -2.73 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 898 HIS 0.008 0.001 HIS D 185 PHE 0.028 0.002 PHE C 752 TYR 0.022 0.002 TYR D 787 ARG 0.006 0.001 ARG C1079 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 453 time to evaluate : 3.568 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: A 197 ARG cc_start: 0.8626 (ttp-110) cc_final: 0.8308 (ttp-110) REVERT: A 201 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8397 (tp) REVERT: A 304 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: A 353 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7630 (pmm) REVERT: A 472 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9033 (mmmm) REVERT: A 723 LEU cc_start: 0.7838 (mm) cc_final: 0.7496 (tt) REVERT: A 789 ASN cc_start: 0.8717 (OUTLIER) cc_final: 0.8049 (t0) REVERT: A 801 MET cc_start: 0.8295 (ppp) cc_final: 0.8090 (ptp) REVERT: A 931 PHE cc_start: 0.8555 (m-80) cc_final: 0.8283 (m-80) REVERT: A 955 ILE cc_start: 0.9279 (tp) cc_final: 0.9001 (tt) REVERT: B 197 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8504 (ttp-110) REVERT: B 201 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8219 (tp) REVERT: B 356 GLU cc_start: 0.9374 (pt0) cc_final: 0.9015 (mp0) REVERT: B 364 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7761 (tmt170) REVERT: B 789 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8218 (t0) REVERT: B 1023 MET cc_start: 0.5665 (mmm) cc_final: 0.5277 (mmm) REVERT: C 189 MET cc_start: 0.7890 (mpp) cc_final: 0.7520 (mpp) REVERT: C 364 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7827 (mtm180) REVERT: C 789 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8140 (t0) REVERT: C 801 MET cc_start: 0.8300 (ppp) cc_final: 0.8082 (ptp) REVERT: C 863 MET cc_start: 0.8577 (mmt) cc_final: 0.8324 (mmt) REVERT: D 189 MET cc_start: 0.7878 (mpp) cc_final: 0.7544 (mpp) REVERT: D 801 MET cc_start: 0.8516 (ptm) cc_final: 0.8314 (ptp) REVERT: D 863 MET cc_start: 0.8610 (mmt) cc_final: 0.8363 (mmt) REVERT: D 978 MET cc_start: 0.7954 (mmt) cc_final: 0.7676 (mmt) REVERT: D 1023 MET cc_start: 0.5660 (mmm) cc_final: 0.5247 (mmm) outliers start: 116 outliers final: 54 residues processed: 536 average time/residue: 0.4180 time to fit residues: 358.7046 Evaluate side-chains 462 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 400 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 472 LYS Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 787 TYR Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 789 ASN Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 787 TYR Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 991 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 37 optimal weight: 0.2980 chunk 161 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 339 optimal weight: 5.9990 chunk 359 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 321 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN B 199 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN C 438 GLN C 483 ASN C 572 ASN ** C 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31188 Z= 0.170 Angle : 0.561 7.726 42252 Z= 0.292 Chirality : 0.039 0.184 4708 Planarity : 0.004 0.051 5280 Dihedral : 5.440 57.364 4024 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.04 % Allowed : 15.23 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3656 helix: 0.89 (0.11), residues: 2396 sheet: -1.60 (0.31), residues: 184 loop : -2.50 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 898 HIS 0.005 0.001 HIS A1080 PHE 0.022 0.001 PHE A 155 TYR 0.020 0.001 TYR B 646 ARG 0.009 0.000 ARG D1079 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 461 time to evaluate : 3.807 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: A 201 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8443 (tp) REVERT: A 304 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7766 (m-80) REVERT: A 435 GLU cc_start: 0.8367 (tp30) cc_final: 0.8088 (tp30) REVERT: A 723 LEU cc_start: 0.7821 (mm) cc_final: 0.7524 (tt) REVERT: A 725 TRP cc_start: 0.7820 (t60) cc_final: 0.7586 (t60) REVERT: A 974 LEU cc_start: 0.8738 (tp) cc_final: 0.8523 (tp) REVERT: B 189 MET cc_start: 0.7582 (mpp) cc_final: 0.7344 (mpp) REVERT: B 197 ARG cc_start: 0.8708 (ttp-110) cc_final: 0.8463 (ttp-110) REVERT: B 201 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8019 (tp) REVERT: B 364 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7757 (tmt170) REVERT: B 789 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 860 LEU cc_start: 0.9308 (tp) cc_final: 0.9073 (tp) REVERT: B 1023 MET cc_start: 0.5718 (mmm) cc_final: 0.5327 (mmm) REVERT: C 186 TYR cc_start: 0.7198 (m-80) cc_final: 0.6948 (m-80) REVERT: C 189 MET cc_start: 0.7942 (mpp) cc_final: 0.7711 (mpp) REVERT: C 364 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.7835 (mtm180) REVERT: C 740 TRP cc_start: 0.7673 (t-100) cc_final: 0.7354 (t-100) REVERT: C 789 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8205 (t0) REVERT: C 860 LEU cc_start: 0.9302 (tp) cc_final: 0.9072 (tp) REVERT: C 863 MET cc_start: 0.8499 (mmt) cc_final: 0.8232 (mmt) REVERT: C 1051 GLU cc_start: 0.8444 (tp30) cc_final: 0.8030 (tp30) REVERT: C 1078 MET cc_start: 0.6329 (mmt) cc_final: 0.5914 (mmt) REVERT: D 201 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7712 (tp) REVERT: D 364 ARG cc_start: 0.7737 (tmm160) cc_final: 0.6690 (tmm-80) REVERT: D 396 MET cc_start: 0.6985 (mmp) cc_final: 0.6690 (mmt) REVERT: D 740 TRP cc_start: 0.7677 (t-100) cc_final: 0.7364 (t-100) REVERT: D 788 MET cc_start: 0.7861 (tmm) cc_final: 0.7548 (tmm) REVERT: D 863 MET cc_start: 0.8496 (mmt) cc_final: 0.8238 (mmt) REVERT: D 1023 MET cc_start: 0.5679 (mmm) cc_final: 0.5248 (mmm) outliers start: 68 outliers final: 44 residues processed: 501 average time/residue: 0.4213 time to fit residues: 338.4404 Evaluate side-chains 463 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 413 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 789 ASN Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 572 ASN Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 789 ASN Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 0.9990 chunk 148 optimal weight: 0.0020 chunk 306 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN B 257 HIS B 268 HIS B1062 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1062 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 973 ASN D1062 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31188 Z= 0.195 Angle : 0.563 9.353 42252 Z= 0.291 Chirality : 0.039 0.172 4708 Planarity : 0.003 0.048 5280 Dihedral : 5.220 59.238 4024 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.40 % Allowed : 15.41 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3656 helix: 1.08 (0.11), residues: 2428 sheet: -1.50 (0.33), residues: 184 loop : -2.41 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 898 HIS 0.003 0.001 HIS C1080 PHE 0.025 0.001 PHE A 155 TYR 0.015 0.001 TYR C 787 ARG 0.008 0.000 ARG A1081 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 436 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8554 (ttp-110) cc_final: 0.8187 (ttp-110) REVERT: A 201 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 723 LEU cc_start: 0.7833 (mm) cc_final: 0.7564 (tt) REVERT: A 789 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8173 (t0) REVERT: B 189 MET cc_start: 0.7586 (mpp) cc_final: 0.7375 (mpp) REVERT: B 197 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8456 (ttp-110) REVERT: B 201 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.7941 (tp) REVERT: B 364 ARG cc_start: 0.8118 (mtm180) cc_final: 0.7802 (tmt170) REVERT: B 689 ASP cc_start: 0.7372 (p0) cc_final: 0.7160 (p0) REVERT: B 860 LEU cc_start: 0.9358 (tp) cc_final: 0.9139 (tp) REVERT: B 1023 MET cc_start: 0.5715 (mmm) cc_final: 0.5321 (mmm) REVERT: C 186 TYR cc_start: 0.7334 (m-80) cc_final: 0.6994 (m-80) REVERT: C 189 MET cc_start: 0.7868 (mpp) cc_final: 0.7643 (mpp) REVERT: C 201 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7364 (tp) REVERT: C 364 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8135 (tmm160) REVERT: C 740 TRP cc_start: 0.7693 (t-100) cc_final: 0.7364 (t-100) REVERT: C 860 LEU cc_start: 0.9314 (tp) cc_final: 0.9092 (tp) REVERT: C 863 MET cc_start: 0.8515 (mmt) cc_final: 0.8169 (mmt) REVERT: C 1051 GLU cc_start: 0.8475 (tp30) cc_final: 0.8088 (tp30) REVERT: C 1078 MET cc_start: 0.6544 (mmt) cc_final: 0.6051 (mmt) REVERT: D 201 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7735 (tp) REVERT: D 304 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: D 740 TRP cc_start: 0.7692 (t-100) cc_final: 0.7355 (t-100) REVERT: D 788 MET cc_start: 0.7846 (tmm) cc_final: 0.7607 (tmm) REVERT: D 822 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8326 (mttp) REVERT: D 863 MET cc_start: 0.8499 (mmt) cc_final: 0.8182 (mmt) REVERT: D 1023 MET cc_start: 0.5674 (mmm) cc_final: 0.5239 (mmm) outliers start: 80 outliers final: 50 residues processed: 490 average time/residue: 0.4118 time to fit residues: 323.0097 Evaluate side-chains 457 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 401 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 516 TYR Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 516 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 0.5980 chunk 323 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 990 ASN A1090 ASN B 268 HIS B 279 ASN B 789 ASN B1090 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN C1090 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN D1090 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 31188 Z= 0.372 Angle : 0.665 8.985 42252 Z= 0.348 Chirality : 0.044 0.185 4708 Planarity : 0.004 0.071 5280 Dihedral : 5.439 56.981 4024 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.49 % Allowed : 14.99 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3656 helix: 0.91 (0.11), residues: 2464 sheet: -1.47 (0.34), residues: 184 loop : -2.35 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 898 HIS 0.004 0.001 HIS D 667 PHE 0.028 0.002 PHE A 155 TYR 0.026 0.002 TYR A 726 ARG 0.012 0.001 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 410 time to evaluate : 3.578 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: A 201 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 304 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: A 723 LEU cc_start: 0.8042 (mm) cc_final: 0.7661 (tt) REVERT: A 789 ASN cc_start: 0.8811 (OUTLIER) cc_final: 0.8341 (t0) REVERT: A 859 MET cc_start: 0.8635 (ptp) cc_final: 0.8189 (ptp) REVERT: A 918 ASP cc_start: 0.8198 (p0) cc_final: 0.7791 (p0) REVERT: B 161 MET cc_start: 0.7701 (mmm) cc_final: 0.7494 (mmm) REVERT: B 201 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 364 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7812 (tmt170) REVERT: B 740 TRP cc_start: 0.7924 (t-100) cc_final: 0.7683 (t-100) REVERT: B 788 MET cc_start: 0.7974 (tmm) cc_final: 0.7653 (tmm) REVERT: B 918 ASP cc_start: 0.8178 (p0) cc_final: 0.7841 (p0) REVERT: B 1023 MET cc_start: 0.5817 (mmm) cc_final: 0.5452 (mmm) REVERT: C 186 TYR cc_start: 0.7475 (m-80) cc_final: 0.6991 (m-80) REVERT: C 201 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7305 (tp) REVERT: C 364 ARG cc_start: 0.8503 (mtm-85) cc_final: 0.8191 (tmm160) REVERT: C 396 MET cc_start: 0.7203 (mmt) cc_final: 0.6954 (mmt) REVERT: C 788 MET cc_start: 0.8032 (tmm) cc_final: 0.7688 (tmm) REVERT: C 863 MET cc_start: 0.8512 (mmt) cc_final: 0.8165 (mmt) REVERT: C 1051 GLU cc_start: 0.8494 (tp30) cc_final: 0.8149 (tp30) REVERT: D 189 MET cc_start: 0.7645 (mpp) cc_final: 0.7413 (mpp) REVERT: D 201 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7766 (tp) REVERT: D 364 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7599 (ttt-90) REVERT: D 569 ILE cc_start: 0.9470 (OUTLIER) cc_final: 0.9262 (tp) REVERT: D 788 MET cc_start: 0.7944 (tmm) cc_final: 0.7719 (tmm) REVERT: D 863 MET cc_start: 0.8539 (mmt) cc_final: 0.8216 (mmt) REVERT: D 918 ASP cc_start: 0.8192 (p0) cc_final: 0.7914 (p0) REVERT: D 1023 MET cc_start: 0.5543 (mmm) cc_final: 0.5085 (mmm) outliers start: 116 outliers final: 84 residues processed: 493 average time/residue: 0.4132 time to fit residues: 325.8221 Evaluate side-chains 474 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 383 time to evaluate : 3.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 585 LYS Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 585 LYS Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 353 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 597 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1069 THR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 353 MET Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 469 ASP Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 723 LEU Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 878 MET Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 991 ASP Chi-restraints excluded: chain D residue 1067 ILE Chi-restraints excluded: chain D residue 1069 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 302 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 358 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN A 279 ASN A 990 ASN B 268 HIS ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31188 Z= 0.208 Angle : 0.582 10.044 42252 Z= 0.301 Chirality : 0.040 0.180 4708 Planarity : 0.004 0.048 5280 Dihedral : 5.196 55.608 4024 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.82 % Allowed : 16.38 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3656 helix: 1.15 (0.11), residues: 2460 sheet: -1.42 (0.34), residues: 184 loop : -2.26 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 898 HIS 0.010 0.001 HIS D 185 PHE 0.029 0.001 PHE A 155 TYR 0.020 0.001 TYR D 186 ARG 0.007 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 425 time to evaluate : 3.532 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: A 197 ARG cc_start: 0.8743 (ttp-110) cc_final: 0.8445 (ttp-110) REVERT: A 201 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8194 (tp) REVERT: A 304 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: A 723 LEU cc_start: 0.8051 (mm) cc_final: 0.7682 (tt) REVERT: A 789 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8275 (t0) REVERT: A 918 ASP cc_start: 0.8074 (p0) cc_final: 0.7591 (p0) REVERT: B 161 MET cc_start: 0.7692 (mmm) cc_final: 0.7470 (mmm) REVERT: B 201 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.7998 (tp) REVERT: B 252 ILE cc_start: 0.7922 (tt) cc_final: 0.7699 (tt) REVERT: B 364 ARG cc_start: 0.8116 (mtm180) cc_final: 0.7848 (tmt170) REVERT: B 788 MET cc_start: 0.7909 (tmm) cc_final: 0.7620 (tmm) REVERT: B 801 MET cc_start: 0.8405 (ppp) cc_final: 0.8152 (ptp) REVERT: B 822 LYS cc_start: 0.8564 (mmmt) cc_final: 0.8293 (mttp) REVERT: B 918 ASP cc_start: 0.8100 (p0) cc_final: 0.7727 (p0) REVERT: B 1023 MET cc_start: 0.5791 (mmm) cc_final: 0.5409 (mmm) REVERT: C 186 TYR cc_start: 0.7305 (m-80) cc_final: 0.6943 (m-80) REVERT: C 201 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7308 (tp) REVERT: C 364 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8184 (tmm160) REVERT: C 396 MET cc_start: 0.7221 (mmt) cc_final: 0.6899 (mmt) REVERT: C 697 LEU cc_start: 0.8975 (tt) cc_final: 0.8718 (tt) REVERT: C 788 MET cc_start: 0.7966 (tmm) cc_final: 0.7644 (tmm) REVERT: C 860 LEU cc_start: 0.9365 (tp) cc_final: 0.9153 (tp) REVERT: C 863 MET cc_start: 0.8446 (mmt) cc_final: 0.8088 (mmt) REVERT: C 1013 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7474 (t80) REVERT: C 1051 GLU cc_start: 0.8472 (tp30) cc_final: 0.8167 (tp30) REVERT: C 1078 MET cc_start: 0.6475 (mmt) cc_final: 0.6206 (mmt) REVERT: D 189 MET cc_start: 0.7895 (mpp) cc_final: 0.7496 (mpp) REVERT: D 201 ILE cc_start: 0.7973 (OUTLIER) cc_final: 0.7748 (tp) REVERT: D 304 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 822 LYS cc_start: 0.8537 (mmmt) cc_final: 0.8327 (mtmt) REVERT: D 863 MET cc_start: 0.8447 (mmt) cc_final: 0.8037 (mmt) REVERT: D 918 ASP cc_start: 0.8116 (p0) cc_final: 0.7500 (p0) REVERT: D 1023 MET cc_start: 0.5517 (mmm) cc_final: 0.5066 (mmm) outliers start: 94 outliers final: 59 residues processed: 488 average time/residue: 0.4153 time to fit residues: 325.1297 Evaluate side-chains 453 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 386 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1067 ILE Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 chunk 214 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 281 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS ** B 741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31188 Z= 0.204 Angle : 0.580 8.586 42252 Z= 0.299 Chirality : 0.040 0.181 4708 Planarity : 0.004 0.046 5280 Dihedral : 5.087 55.829 4024 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.85 % Allowed : 16.47 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.14), residues: 3656 helix: 1.27 (0.11), residues: 2460 sheet: -1.41 (0.34), residues: 184 loop : -2.15 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 898 HIS 0.009 0.001 HIS D 185 PHE 0.029 0.001 PHE A 155 TYR 0.015 0.001 TYR D 787 ARG 0.005 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 410 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8471 (ttp-110) REVERT: A 201 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 304 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7826 (m-80) REVERT: A 364 ARG cc_start: 0.7895 (tmt170) cc_final: 0.7433 (ttp-170) REVERT: A 723 LEU cc_start: 0.8062 (mm) cc_final: 0.7699 (tt) REVERT: A 789 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8181 (t0) REVERT: A 918 ASP cc_start: 0.8111 (p0) cc_final: 0.7626 (p0) REVERT: A 1013 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7614 (t80) REVERT: B 161 MET cc_start: 0.7708 (mmm) cc_final: 0.7485 (mmm) REVERT: B 201 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 364 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7887 (tmt170) REVERT: B 740 TRP cc_start: 0.7843 (t-100) cc_final: 0.7576 (t-100) REVERT: B 788 MET cc_start: 0.7889 (tmm) cc_final: 0.7617 (tmm) REVERT: B 822 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8300 (mtmt) REVERT: B 918 ASP cc_start: 0.8080 (p0) cc_final: 0.7690 (p0) REVERT: B 1023 MET cc_start: 0.5852 (mmm) cc_final: 0.5457 (mmm) REVERT: C 186 TYR cc_start: 0.7256 (m-80) cc_final: 0.6906 (m-80) REVERT: C 201 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7216 (tp) REVERT: C 304 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7855 (m-80) REVERT: C 364 ARG cc_start: 0.8499 (mtm-85) cc_final: 0.8262 (tmm160) REVERT: C 396 MET cc_start: 0.7204 (mmt) cc_final: 0.6908 (mmt) REVERT: C 697 LEU cc_start: 0.8983 (tt) cc_final: 0.8716 (tt) REVERT: C 788 MET cc_start: 0.7943 (tmm) cc_final: 0.7639 (tmm) REVERT: C 822 LYS cc_start: 0.8534 (mmmt) cc_final: 0.8314 (mtmt) REVERT: C 860 LEU cc_start: 0.9363 (tp) cc_final: 0.9156 (tp) REVERT: C 1013 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7491 (t80) REVERT: C 1051 GLU cc_start: 0.8449 (tp30) cc_final: 0.8146 (tp30) REVERT: C 1078 MET cc_start: 0.6593 (mmt) cc_final: 0.6186 (mmt) REVERT: D 189 MET cc_start: 0.7903 (mpp) cc_final: 0.7501 (mpp) REVERT: D 201 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7718 (tp) REVERT: D 304 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: D 863 MET cc_start: 0.8449 (mmt) cc_final: 0.8078 (mmt) REVERT: D 918 ASP cc_start: 0.8113 (p0) cc_final: 0.7487 (p0) REVERT: D 1013 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7659 (t80) REVERT: D 1023 MET cc_start: 0.5514 (mmm) cc_final: 0.5060 (mmm) outliers start: 95 outliers final: 69 residues processed: 469 average time/residue: 0.4223 time to fit residues: 322.3639 Evaluate side-chains 471 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 391 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 334 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 301 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 332 optimal weight: 0.0870 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 HIS B 990 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 572 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31188 Z= 0.203 Angle : 0.588 13.083 42252 Z= 0.301 Chirality : 0.040 0.182 4708 Planarity : 0.004 0.047 5280 Dihedral : 5.042 56.136 4024 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.82 % Allowed : 16.56 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.14), residues: 3656 helix: 1.34 (0.11), residues: 2452 sheet: -1.41 (0.34), residues: 184 loop : -2.11 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 453 HIS 0.008 0.001 HIS D 185 PHE 0.028 0.001 PHE B 155 TYR 0.014 0.001 TYR C 787 ARG 0.008 0.000 ARG D 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 410 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ARG cc_start: 0.8680 (ttp-110) cc_final: 0.8478 (ttp-110) REVERT: A 201 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8400 (tp) REVERT: A 304 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: A 364 ARG cc_start: 0.7949 (tmt170) cc_final: 0.7552 (ttp-170) REVERT: A 723 LEU cc_start: 0.8134 (mm) cc_final: 0.7842 (tt) REVERT: A 789 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8367 (t0) REVERT: A 918 ASP cc_start: 0.8104 (p0) cc_final: 0.7618 (p0) REVERT: A 1013 PHE cc_start: 0.7962 (OUTLIER) cc_final: 0.7647 (t80) REVERT: B 161 MET cc_start: 0.7733 (mmm) cc_final: 0.7490 (mmm) REVERT: B 201 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.7972 (tp) REVERT: B 441 LEU cc_start: 0.9213 (mp) cc_final: 0.8607 (mm) REVERT: B 740 TRP cc_start: 0.7915 (t-100) cc_final: 0.7656 (t-100) REVERT: B 788 MET cc_start: 0.7882 (tmm) cc_final: 0.7605 (tmm) REVERT: B 918 ASP cc_start: 0.8129 (p0) cc_final: 0.7732 (p0) REVERT: B 1023 MET cc_start: 0.5863 (mmm) cc_final: 0.5452 (mmm) REVERT: B 1051 GLU cc_start: 0.8315 (tp30) cc_final: 0.7798 (tp30) REVERT: B 1082 PHE cc_start: 0.7509 (m-10) cc_final: 0.7040 (m-10) REVERT: C 186 TYR cc_start: 0.7270 (m-80) cc_final: 0.6909 (m-80) REVERT: C 201 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7153 (tp) REVERT: C 304 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.7822 (m-80) REVERT: C 396 MET cc_start: 0.7227 (mmt) cc_final: 0.6835 (mmt) REVERT: C 697 LEU cc_start: 0.8990 (tt) cc_final: 0.8724 (tt) REVERT: C 788 MET cc_start: 0.7935 (tmm) cc_final: 0.7628 (tmm) REVERT: C 822 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8301 (mtmt) REVERT: C 860 LEU cc_start: 0.9362 (tp) cc_final: 0.9154 (tp) REVERT: C 1051 GLU cc_start: 0.8419 (tp30) cc_final: 0.8099 (tp30) REVERT: C 1078 MET cc_start: 0.6592 (mmt) cc_final: 0.6207 (mmt) REVERT: D 189 MET cc_start: 0.7893 (mpp) cc_final: 0.7511 (mpp) REVERT: D 201 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7550 (tp) REVERT: D 304 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: D 863 MET cc_start: 0.8433 (mmt) cc_final: 0.8059 (mmt) REVERT: D 1013 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7709 (t80) REVERT: D 1023 MET cc_start: 0.5506 (mmm) cc_final: 0.5059 (mmm) outliers start: 94 outliers final: 72 residues processed: 465 average time/residue: 0.4096 time to fit residues: 308.9210 Evaluate side-chains 472 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 390 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 440 ASP Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 787 TYR Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.6980 chunk 353 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 30.0000 chunk 341 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 227 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 HIS B 268 HIS B 990 ASN ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 572 ASN ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31188 Z= 0.184 Angle : 0.579 12.974 42252 Z= 0.298 Chirality : 0.039 0.172 4708 Planarity : 0.004 0.048 5280 Dihedral : 4.974 55.857 4024 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.43 % Allowed : 17.22 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3656 helix: 1.41 (0.11), residues: 2452 sheet: -1.39 (0.34), residues: 184 loop : -2.02 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 898 HIS 0.007 0.001 HIS D 185 PHE 0.034 0.001 PHE D 155 TYR 0.033 0.001 TYR C 646 ARG 0.008 0.000 ARG C 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 411 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8009 (mmm) cc_final: 0.7797 (mmp) REVERT: A 201 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 304 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: A 364 ARG cc_start: 0.7965 (tmt170) cc_final: 0.7131 (ttp-170) REVERT: A 723 LEU cc_start: 0.8067 (mm) cc_final: 0.7812 (tt) REVERT: A 789 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8321 (t0) REVERT: A 918 ASP cc_start: 0.8100 (p0) cc_final: 0.7615 (p0) REVERT: A 1013 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7592 (t80) REVERT: B 161 MET cc_start: 0.7694 (mmm) cc_final: 0.7454 (mmm) REVERT: B 201 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.7886 (tp) REVERT: B 740 TRP cc_start: 0.7909 (t-100) cc_final: 0.7660 (t-100) REVERT: B 788 MET cc_start: 0.7877 (tmm) cc_final: 0.7598 (tmm) REVERT: B 918 ASP cc_start: 0.8049 (p0) cc_final: 0.7645 (p0) REVERT: B 978 MET cc_start: 0.7996 (mpp) cc_final: 0.7758 (mpp) REVERT: B 1023 MET cc_start: 0.5916 (mmm) cc_final: 0.5387 (mmm) REVERT: B 1051 GLU cc_start: 0.8272 (tp30) cc_final: 0.7729 (tp30) REVERT: B 1082 PHE cc_start: 0.7505 (m-10) cc_final: 0.7079 (m-10) REVERT: C 186 TYR cc_start: 0.7310 (m-80) cc_final: 0.7044 (m-80) REVERT: C 304 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: C 396 MET cc_start: 0.7250 (mmt) cc_final: 0.6861 (mmt) REVERT: C 402 GLU cc_start: 0.8088 (pp20) cc_final: 0.7802 (pp20) REVERT: C 697 LEU cc_start: 0.8995 (tt) cc_final: 0.8715 (tt) REVERT: C 788 MET cc_start: 0.7930 (tmm) cc_final: 0.7634 (tmm) REVERT: C 860 LEU cc_start: 0.9347 (tp) cc_final: 0.9141 (tp) REVERT: C 1013 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 1051 GLU cc_start: 0.8373 (tp30) cc_final: 0.8030 (tp30) REVERT: C 1078 MET cc_start: 0.6614 (mmt) cc_final: 0.6229 (mmt) REVERT: D 189 MET cc_start: 0.7862 (mpp) cc_final: 0.7494 (mpp) REVERT: D 201 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.6561 (tp) REVERT: D 304 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: D 863 MET cc_start: 0.8416 (mmt) cc_final: 0.8053 (mmt) REVERT: D 1013 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7672 (t80) REVERT: D 1023 MET cc_start: 0.5505 (mmm) cc_final: 0.5054 (mmm) outliers start: 81 outliers final: 64 residues processed: 459 average time/residue: 0.4031 time to fit residues: 301.8903 Evaluate side-chains 462 residues out of total 3328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 388 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 THR Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 787 TYR Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 849 VAL Chi-restraints excluded: chain A residue 967 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1013 PHE Chi-restraints excluded: chain A residue 1049 ASP Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 584 THR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 755 VAL Chi-restraints excluded: chain B residue 783 VAL Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain B residue 878 MET Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 990 ASN Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1049 ASP Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 572 ASN Chi-restraints excluded: chain C residue 584 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 849 VAL Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 878 MET Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 967 THR Chi-restraints excluded: chain C residue 990 ASN Chi-restraints excluded: chain C residue 1013 PHE Chi-restraints excluded: chain C residue 1049 ASP Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 783 VAL Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 925 ASP Chi-restraints excluded: chain D residue 967 THR Chi-restraints excluded: chain D residue 990 ASN Chi-restraints excluded: chain D residue 1013 PHE Chi-restraints excluded: chain D residue 1049 ASP Chi-restraints excluded: chain D residue 1067 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 7.9990 chunk 314 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 HIS ** C 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.130556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095119 restraints weight = 65142.071| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.04 r_work: 0.3189 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 31188 Z= 0.300 Angle : 0.738 59.000 42252 Z= 0.411 Chirality : 0.041 0.361 4708 Planarity : 0.004 0.121 5280 Dihedral : 4.975 55.855 4024 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.49 % Allowed : 17.43 % Favored : 80.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3656 helix: 1.39 (0.11), residues: 2452 sheet: -1.39 (0.34), residues: 184 loop : -2.02 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP A 798 HIS 0.022 0.001 HIS B 185 PHE 0.031 0.001 PHE D 155 TYR 0.025 0.001 TYR D 646 ARG 0.005 0.000 ARG C 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7168.00 seconds wall clock time: 130 minutes 36.89 seconds (7836.89 seconds total)