Starting phenix.real_space_refine on Tue Mar 19 01:15:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m39_30071/03_2024/6m39_30071.pdb" } resolution = 3.55 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= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14415 2.51 5 N 3771 2.21 5 O 4395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 446": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A ARG 877": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 196": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ARG 470": "NH1" <-> "NH2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 564": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B ARG 652": "NH1" <-> "NH2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 849": "NH1" <-> "NH2" Residue "B ARG 877": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C ARG 196": "NH1" <-> "NH2" Residue "C ARG 249": "NH1" <-> "NH2" Residue "C ARG 296": "NH1" <-> "NH2" Residue "C ARG 446": "NH1" <-> "NH2" Residue "C ARG 470": "NH1" <-> "NH2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C ARG 609": "NH1" <-> "NH2" Residue "C ARG 652": "NH1" <-> "NH2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 849": "NH1" <-> "NH2" Residue "C ARG 877": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22716 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7320 Classifications: {'peptide': 937} Link IDs: {'PTRANS': 39, 'TRANS': 897} Chain breaks: 4 Chain: "B" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7320 Classifications: {'peptide': 937} Link IDs: {'PTRANS': 39, 'TRANS': 897} Chain breaks: 4 Chain: "C" Number of atoms: 7320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 937, 7320 Classifications: {'peptide': 937} Link IDs: {'PTRANS': 39, 'TRANS': 897} Chain breaks: 4 Chain: "A" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "B" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Chain: "C" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 252 Unusual residues: {'NAG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 12.32, per 1000 atoms: 0.54 Number of scatterers: 22716 At special positions: 0 Unit cell: (118.56, 119.6, 158.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4395 8.00 N 3771 7.00 C 14415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 246 " distance=2.01 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 302 " distance=2.01 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 371 " distance=2.02 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 399 " distance=2.04 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 597 " - pdb=" SG CYS A 603 " distance=2.01 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 708 " distance=2.02 Simple disulfide: pdb=" SG CYS A 886 " - pdb=" SG CYS A 897 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 58 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 246 " distance=2.01 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 302 " distance=2.01 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 371 " distance=2.02 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 399 " distance=2.04 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 614 " distance=2.02 Simple disulfide: pdb=" SG CYS B 597 " - pdb=" SG CYS B 603 " distance=2.01 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 708 " distance=2.02 Simple disulfide: pdb=" SG CYS B 886 " - pdb=" SG CYS B 897 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 236 " - pdb=" SG CYS C 246 " distance=2.01 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 302 " distance=2.01 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 371 " distance=2.02 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 399 " distance=2.04 Simple disulfide: pdb=" SG CYS C 592 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 597 " - pdb=" SG CYS C 603 " distance=2.01 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 708 " distance=2.02 Simple disulfide: pdb=" SG CYS C 886 " - pdb=" SG CYS C 897 " distance=2.02 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 Links applied NAG-ASN " NAG A1001 " - " ASN A 654 " " NAG A1002 " - " ASN A 924 " " NAG A1003 " - " ASN A 957 " " NAG A1004 " - " ASN A 973 " " NAG A1005 " - " ASN A 987 " " NAG A1006 " - " ASN A 52 " " NAG A1007 " - " ASN A 992 " " NAG A1008 " - " ASN A 154 " " NAG A1009 " - " ASN A 358 " " NAG A1010 " - " ASN A 520 " " NAG A1011 " - " ASN A 305 " " NAG A1012 " - " ASN A 275 " " NAG A1013 " - " ASN A 39 " " NAG A1014 " - " ASN A 472 " " NAG A1015 " - " ASN A 514 " " NAG A1016 " - " ASN A 503 " " NAG A1017 " - " ASN A 104 " " NAG A1018 " - " ASN A 525 " " NAG B1001 " - " ASN B 654 " " NAG B1002 " - " ASN B 924 " " NAG B1003 " - " ASN B 957 " " NAG B1004 " - " ASN B 973 " " NAG B1005 " - " ASN B 987 " " NAG B1006 " - " ASN B 52 " " NAG B1007 " - " ASN B 992 " " NAG B1008 " - " ASN B 154 " " NAG B1009 " - " ASN B 358 " " NAG B1010 " - " ASN B 520 " " NAG B1011 " - " ASN B 305 " " NAG B1012 " - " ASN B 275 " " NAG B1013 " - " ASN B 39 " " NAG B1014 " - " ASN B 472 " " NAG B1015 " - " ASN B 514 " " NAG B1016 " - " ASN B 503 " " NAG B1017 " - " ASN B 104 " " NAG B1018 " - " ASN B 525 " " NAG C1001 " - " ASN C 654 " " NAG C1002 " - " ASN C 924 " " NAG C1003 " - " ASN C 957 " " NAG C1004 " - " ASN C 973 " " NAG C1005 " - " ASN C 987 " " NAG C1006 " - " ASN C 52 " " NAG C1007 " - " ASN C 992 " " NAG C1008 " - " ASN C 154 " " NAG C1009 " - " ASN C 358 " " NAG C1010 " - " ASN C 520 " " NAG C1011 " - " ASN C 305 " " NAG C1012 " - " ASN C 275 " " NAG C1013 " - " ASN C 39 " " NAG C1014 " - " ASN C 472 " " NAG C1015 " - " ASN C 514 " " NAG C1016 " - " ASN C 503 " " NAG C1017 " - " ASN C 104 " " NAG C1018 " - " ASN C 525 " Time building additional restraints: 8.18 Conformation dependent library (CDL) restraints added in 3.9 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5220 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 21.6% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE A 27 " --> pdb=" O PHE A 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN A 28 " --> pdb=" O ASN A 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 28' Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 503 removed outlier: 3.551A pdb=" N HIS A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 503 " --> pdb=" O PRO A 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 499 through 503' Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 638 Processing helix chain 'A' and resid 676 through 682 Processing helix chain 'A' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 763 Processing helix chain 'A' and resid 770 through 786 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 836 Processing helix chain 'A' and resid 841 through 887 removed outlier: 3.773A pdb=" N ARG A 849 " --> pdb=" O VAL A 845 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 853 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 856 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN B 28 " --> pdb=" O ASN B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.552A pdb=" N HIS B 502 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN B 503 " --> pdb=" O PRO B 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 503' Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS B 604 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 606 " --> pdb=" O ALA B 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 676 through 682 Processing helix chain 'B' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 763 Processing helix chain 'B' and resid 770 through 786 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 836 Processing helix chain 'B' and resid 841 through 887 removed outlier: 3.774A pdb=" N ARG B 849 " --> pdb=" O VAL B 845 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 853 " --> pdb=" O ARG B 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN B 856 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.518A pdb=" N PHE C 27 " --> pdb=" O PHE C 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 28 " --> pdb=" O ASN C 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 24 through 28' Processing helix chain 'C' and resid 171 through 173 No H-bonds generated for 'chain 'C' and resid 171 through 173' Processing helix chain 'C' and resid 240 through 248 removed outlier: 3.637A pdb=" N LEU C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.751A pdb=" N LYS C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 503 removed outlier: 3.551A pdb=" N HIS C 502 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 503 " --> pdb=" O PRO C 500 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 499 through 503' Processing helix chain 'C' and resid 591 through 596 Processing helix chain 'C' and resid 600 through 608 removed outlier: 4.260A pdb=" N LYS C 604 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU C 606 " --> pdb=" O ALA C 602 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 638 Processing helix chain 'C' and resid 676 through 682 Processing helix chain 'C' and resid 690 through 702 removed outlier: 3.743A pdb=" N ASN C 701 " --> pdb=" O ASN C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 763 Processing helix chain 'C' and resid 770 through 786 Processing helix chain 'C' and resid 787 through 789 No H-bonds generated for 'chain 'C' and resid 787 through 789' Processing helix chain 'C' and resid 798 through 822 removed outlier: 3.553A pdb=" N ILE C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE C 820 " --> pdb=" O LEU C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 836 Processing helix chain 'C' and resid 841 through 887 removed outlier: 3.774A pdb=" N ARG C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY C 853 " --> pdb=" O ARG C 849 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 856 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 885 " --> pdb=" O SER C 881 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.242A pdb=" N ARG A 232 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70 removed outlier: 7.261A pdb=" N TRP A 110 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL A 123 " --> pdb=" O TRP A 110 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N HIS A 112 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 121 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 removed outlier: 3.600A pdb=" N GLY A 168 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A 165 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A 77 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG A 210 " --> pdb=" O GLN A 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL A 257 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR A 469 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER A 259 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 467 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 512 " --> pdb=" O THR A 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR A 505 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 415 removed outlier: 3.597A pdb=" N LYS A 453 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG A 446 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER A 459 " --> pdb=" O GLN A 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN A 444 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 441 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A 447 " --> pdb=" O LEU A 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 522 through 523 removed outlier: 3.636A pdb=" N ALA A 543 " --> pdb=" O ASP A 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 567 through 582 removed outlier: 6.942A pdb=" N ASN A 925 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS A 572 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 574 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU A 921 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU A 576 " --> pdb=" O TYR A 919 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR A 919 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU A 578 " --> pdb=" O PHE A 917 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 917 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE A 580 " --> pdb=" O MET A 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET A 915 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 582 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY A 913 " --> pdb=" O GLN A 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A 921 " --> pdb=" O HIS A 902 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS A 902 " --> pdb=" O LEU A 921 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 587 through 590 Processing sheet with id=AB1, first strand: chain 'A' and resid 979 through 981 Processing sheet with id=AB2, first strand: chain 'A' and resid 952 through 954 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.242A pdb=" N ARG B 232 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 67 through 70 removed outlier: 7.261A pdb=" N TRP B 110 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N VAL B 123 " --> pdb=" O TRP B 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS B 112 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL B 121 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 186 through 188 removed outlier: 3.601A pdb=" N GLY B 168 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR B 165 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 77 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ARG B 210 " --> pdb=" O GLN B 77 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL B 257 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR B 469 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N SER B 259 " --> pdb=" O VAL B 467 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 467 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 512 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 505 " --> pdb=" O LEU B 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 297 through 299 Processing sheet with id=AB8, first strand: chain 'B' and resid 413 through 415 removed outlier: 3.597A pdb=" N LYS B 453 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG B 446 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER B 459 " --> pdb=" O GLN B 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN B 444 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 441 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 447 " --> pdb=" O LEU B 439 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 522 through 523 removed outlier: 3.638A pdb=" N ALA B 543 " --> pdb=" O ASP B 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 567 through 582 removed outlier: 6.943A pdb=" N ASN B 925 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS B 572 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 574 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 921 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 576 " --> pdb=" O TYR B 919 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR B 919 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU B 578 " --> pdb=" O PHE B 917 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N PHE B 917 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE B 580 " --> pdb=" O MET B 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET B 915 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN B 582 " --> pdb=" O GLY B 913 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY B 913 " --> pdb=" O GLN B 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 913 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 921 " --> pdb=" O HIS B 902 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS B 902 " --> pdb=" O LEU B 921 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 587 through 590 Processing sheet with id=AC3, first strand: chain 'B' and resid 979 through 981 Processing sheet with id=AC4, first strand: chain 'B' and resid 952 through 954 Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.243A pdb=" N ARG C 232 " --> pdb=" O GLU C 223 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 67 through 70 removed outlier: 7.260A pdb=" N TRP C 110 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL C 123 " --> pdb=" O TRP C 110 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N HIS C 112 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL C 121 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 186 through 188 removed outlier: 3.600A pdb=" N GLY C 168 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR C 165 " --> pdb=" O THR C 78 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN C 77 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG C 210 " --> pdb=" O GLN C 77 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 256 through 262 removed outlier: 5.643A pdb=" N VAL C 257 " --> pdb=" O TYR C 469 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR C 469 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N SER C 259 " --> pdb=" O VAL C 467 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL C 467 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU C 512 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 505 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 297 through 299 Processing sheet with id=AD1, first strand: chain 'C' and resid 413 through 415 removed outlier: 3.598A pdb=" N LYS C 453 " --> pdb=" O ILE C 450 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ARG C 446 " --> pdb=" O VAL C 457 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N SER C 459 " --> pdb=" O GLN C 444 " (cutoff:3.500A) removed outlier: 13.181A pdb=" N GLN C 444 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 441 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR C 447 " --> pdb=" O LEU C 439 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 522 through 523 removed outlier: 3.637A pdb=" N ALA C 543 " --> pdb=" O ASP C 537 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 567 through 582 removed outlier: 6.943A pdb=" N ASN C 925 " --> pdb=" O LEU C 570 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N HIS C 572 " --> pdb=" O PRO C 923 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 574 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 921 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU C 576 " --> pdb=" O TYR C 919 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C 919 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU C 578 " --> pdb=" O PHE C 917 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE C 917 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE C 580 " --> pdb=" O MET C 915 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET C 915 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN C 582 " --> pdb=" O GLY C 913 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY C 913 " --> pdb=" O GLN C 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 913 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 921 " --> pdb=" O HIS C 902 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS C 902 " --> pdb=" O LEU C 921 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 587 through 590 Processing sheet with id=AD5, first strand: chain 'C' and resid 979 through 981 Processing sheet with id=AD6, first strand: chain 'C' and resid 952 through 954 687 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.46 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6987 1.34 - 1.46: 5940 1.46 - 1.58: 10122 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 23229 Sorted by residual: bond pdb=" CB ILE A 802 " pdb=" CG2 ILE A 802 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 7.93e+00 bond pdb=" CB ILE B 802 " pdb=" CG2 ILE B 802 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" CB ILE C 802 " pdb=" CG2 ILE C 802 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.79e+00 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" C1 NAG C1006 " pdb=" O5 NAG C1006 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 23224 not shown) Histogram of bond angle deviations from ideal: 96.20 - 103.78: 287 103.78 - 111.36: 9441 111.36 - 118.93: 9095 118.93 - 126.51: 12426 126.51 - 134.09: 371 Bond angle restraints: 31620 Sorted by residual: angle pdb=" N VAL A 392 " pdb=" CA VAL A 392 " pdb=" C VAL A 392 " ideal model delta sigma weight residual 106.21 113.15 -6.94 1.07e+00 8.73e-01 4.20e+01 angle pdb=" N VAL B 392 " pdb=" CA VAL B 392 " pdb=" C VAL B 392 " ideal model delta sigma weight residual 106.21 113.14 -6.93 1.07e+00 8.73e-01 4.19e+01 angle pdb=" N VAL C 392 " pdb=" CA VAL C 392 " pdb=" C VAL C 392 " ideal model delta sigma weight residual 106.21 113.10 -6.89 1.07e+00 8.73e-01 4.15e+01 angle pdb=" C HIS C 712 " pdb=" N ASN C 713 " pdb=" CA ASN C 713 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C HIS A 712 " pdb=" N ASN A 713 " pdb=" CA ASN A 713 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 ... (remaining 31615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.99: 13625 20.99 - 41.98: 641 41.98 - 62.98: 101 62.98 - 83.97: 12 83.97 - 104.96: 24 Dihedral angle restraints: 14403 sinusoidal: 6255 harmonic: 8148 Sorted by residual: dihedral pdb=" CB CYS C 287 " pdb=" SG CYS C 287 " pdb=" SG CYS C 292 " pdb=" CB CYS C 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.40 -60.40 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS B 287 " pdb=" SG CYS B 287 " pdb=" SG CYS B 292 " pdb=" CB CYS B 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.39 -60.39 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS A 287 " pdb=" SG CYS A 287 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual 93.00 153.35 -60.35 1 1.00e+01 1.00e-02 4.85e+01 ... (remaining 14400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3069 0.090 - 0.181: 599 0.181 - 0.271: 43 0.271 - 0.361: 6 0.361 - 0.452: 9 Chirality restraints: 3726 Sorted by residual: chirality pdb=" C1 NAG B1007 " pdb=" ND2 ASN B 992 " pdb=" C2 NAG B1007 " pdb=" O5 NAG B1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1 NAG C1007 " pdb=" ND2 ASN C 992 " pdb=" C2 NAG C1007 " pdb=" O5 NAG C1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" C1 NAG A1007 " pdb=" ND2 ASN A 992 " pdb=" C2 NAG A1007 " pdb=" O5 NAG A1007 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 3723 not shown) Planarity restraints: 4044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1018 " 0.044 2.00e-02 2.50e+03 3.64e-02 1.65e+01 pdb=" C7 NAG B1018 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG B1018 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG B1018 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG B1018 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1018 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG A1018 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1018 " 0.033 2.00e-02 2.50e+03 pdb=" N2 NAG A1018 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1018 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1018 " -0.044 2.00e-02 2.50e+03 3.61e-02 1.63e+01 pdb=" C7 NAG C1018 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C1018 " -0.033 2.00e-02 2.50e+03 pdb=" N2 NAG C1018 " 0.057 2.00e-02 2.50e+03 pdb=" O7 NAG C1018 " 0.008 2.00e-02 2.50e+03 ... (remaining 4041 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6094 2.80 - 3.32: 20894 3.32 - 3.85: 37722 3.85 - 4.37: 42393 4.37 - 4.90: 72504 Nonbonded interactions: 179607 Sorted by model distance: nonbonded pdb=" O THR C 584 " pdb=" OG SER C 912 " model vdw 2.271 2.440 nonbonded pdb=" O THR A 584 " pdb=" OG SER A 912 " model vdw 2.272 2.440 nonbonded pdb=" O THR B 584 " pdb=" OG SER B 912 " model vdw 2.273 2.440 nonbonded pdb=" O ALA A 47 " pdb=" OH TYR A 75 " model vdw 2.297 2.440 nonbonded pdb=" O ALA B 47 " pdb=" OH TYR B 75 " model vdw 2.297 2.440 ... (remaining 179602 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.680 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 58.360 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 0.093 23229 Z= 0.621 Angle : 1.263 16.578 31620 Z= 0.667 Chirality : 0.071 0.452 3726 Planarity : 0.007 0.062 3990 Dihedral : 13.057 104.958 9093 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 1.23 % Allowed : 7.39 % Favored : 91.38 % 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: -4.52 (0.12), residues: 2781 helix: -3.53 (0.13), residues: 636 sheet: -2.24 (0.19), residues: 564 loop : -3.16 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP C 110 HIS 0.013 0.004 HIS C 902 PHE 0.040 0.004 PHE A 588 TYR 0.037 0.004 TYR C 436 ARG 0.023 0.002 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 582 time to evaluate : 2.190 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 620 ASP cc_start: 0.8282 (t70) cc_final: 0.7824 (t0) REVERT: A 770 LEU cc_start: 0.8247 (mm) cc_final: 0.8035 (mt) REVERT: B 28 ASN cc_start: 0.8758 (p0) cc_final: 0.8319 (p0) REVERT: B 186 GLU cc_start: 0.6015 (tm-30) cc_final: 0.5749 (tm-30) REVERT: B 210 ARG cc_start: 0.5843 (pmm-80) cc_final: 0.5638 (ptp-170) REVERT: B 370 GLU cc_start: 0.6875 (pt0) cc_final: 0.6649 (pt0) REVERT: B 468 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9207 (pp) REVERT: B 620 ASP cc_start: 0.8513 (t70) cc_final: 0.7900 (t0) REVERT: B 808 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7656 (tt0) REVERT: C 210 ARG cc_start: 0.5725 (pmm-80) cc_final: 0.5487 (ptp-170) REVERT: C 259 SER cc_start: 0.8825 (m) cc_final: 0.8600 (p) REVERT: C 848 ASP cc_start: 0.7669 (t0) cc_final: 0.7289 (t0) outliers start: 30 outliers final: 5 residues processed: 598 average time/residue: 0.3546 time to fit residues: 321.9376 Evaluate side-chains 300 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 294 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 GLN A 319 HIS A 334 ASN A 444 GLN A 488 HIS A 528 ASN A 710 GLN A 809 ASN A 852 ASN A 880 GLN B 101 HIS ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 318 GLN B 319 HIS ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 528 ASN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 783 GLN B 809 ASN B 880 GLN C 101 HIS ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 318 GLN C 319 HIS C 334 ASN C 488 HIS C 528 ASN C 615 GLN C 710 GLN C 809 ASN C 823 ASN C 880 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23229 Z= 0.262 Angle : 0.781 11.662 31620 Z= 0.394 Chirality : 0.049 0.344 3726 Planarity : 0.005 0.049 3990 Dihedral : 9.919 76.013 4191 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.52 % Allowed : 14.20 % Favored : 81.28 % 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: -3.62 (0.14), residues: 2781 helix: -2.25 (0.17), residues: 642 sheet: -1.53 (0.22), residues: 516 loop : -2.88 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 376 HIS 0.005 0.002 HIS B 319 PHE 0.029 0.002 PHE C 608 TYR 0.020 0.002 TYR A 369 ARG 0.009 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 355 time to evaluate : 2.301 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: A 28 ASN cc_start: 0.8733 (p0) cc_final: 0.8141 (p0) REVERT: A 348 VAL cc_start: 0.8471 (p) cc_final: 0.8224 (m) REVERT: A 370 GLU cc_start: 0.7122 (pt0) cc_final: 0.6877 (mt-10) REVERT: A 620 ASP cc_start: 0.8377 (t70) cc_final: 0.8021 (t0) REVERT: A 633 SER cc_start: 0.8895 (t) cc_final: 0.8564 (p) REVERT: A 770 LEU cc_start: 0.8300 (mm) cc_final: 0.8048 (mt) REVERT: B 72 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9199 (pp) REVERT: B 210 ARG cc_start: 0.5968 (pmm-80) cc_final: 0.5176 (ptp90) REVERT: B 301 ASN cc_start: 0.8405 (m-40) cc_final: 0.8016 (m-40) REVERT: B 494 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7646 (t80) REVERT: B 620 ASP cc_start: 0.8456 (t70) cc_final: 0.8034 (t0) REVERT: C 72 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9181 (pp) REVERT: C 348 VAL cc_start: 0.8550 (p) cc_final: 0.8276 (m) REVERT: C 633 SER cc_start: 0.8869 (t) cc_final: 0.8444 (p) REVERT: C 874 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8174 (t160) outliers start: 110 outliers final: 45 residues processed: 441 average time/residue: 0.2980 time to fit residues: 212.6608 Evaluate side-chains 325 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 874 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 0.4980 chunk 78 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 274 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 251 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 203 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN A 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN B 101 HIS ** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN B 528 ASN ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN C 101 HIS ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 GLN C 808 GLN C 880 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 23229 Z= 0.309 Angle : 0.753 11.095 31620 Z= 0.377 Chirality : 0.048 0.335 3726 Planarity : 0.005 0.044 3990 Dihedral : 8.339 58.655 4189 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 5.91 % Allowed : 15.07 % Favored : 79.02 % 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: -3.13 (0.14), residues: 2781 helix: -1.70 (0.18), residues: 639 sheet: -1.40 (0.23), residues: 507 loop : -2.55 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 110 HIS 0.005 0.001 HIS A 502 PHE 0.024 0.002 PHE B 317 TYR 0.020 0.002 TYR C 369 ARG 0.004 0.001 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 296 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 ARG cc_start: 0.6355 (mmm160) cc_final: 0.6149 (mmm160) REVERT: A 620 ASP cc_start: 0.8432 (t70) cc_final: 0.8025 (t0) REVERT: A 633 SER cc_start: 0.8890 (t) cc_final: 0.8554 (p) REVERT: A 770 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 899 GLN cc_start: 0.7026 (mm-40) cc_final: 0.6684 (mm-40) REVERT: B 251 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 269 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 301 ASN cc_start: 0.8618 (m-40) cc_final: 0.8044 (m-40) REVERT: B 370 GLU cc_start: 0.7367 (pt0) cc_final: 0.7000 (pt0) REVERT: B 494 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 498 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8073 (pt) REVERT: B 620 ASP cc_start: 0.8487 (t70) cc_final: 0.8017 (t0) REVERT: B 749 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8400 (mtp) REVERT: C 251 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8370 (m-80) REVERT: C 269 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8184 (tp) REVERT: C 301 ASN cc_start: 0.8446 (m110) cc_final: 0.8129 (m-40) REVERT: C 348 VAL cc_start: 0.8522 (p) cc_final: 0.8316 (m) REVERT: C 633 SER cc_start: 0.8797 (t) cc_final: 0.8428 (p) REVERT: C 874 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8209 (t160) REVERT: C 880 GLN cc_start: 0.7556 (mt0) cc_final: 0.7327 (mt0) outliers start: 144 outliers final: 74 residues processed: 409 average time/residue: 0.2952 time to fit residues: 198.8846 Evaluate side-chains 348 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 265 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 749 MET Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 251 PHE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 6.9990 chunk 269 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS A 528 ASN A 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 502 HIS B 528 ASN B 552 HIS B 710 GLN B 880 GLN C 101 HIS ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 23229 Z= 0.310 Angle : 0.737 9.767 31620 Z= 0.369 Chirality : 0.048 0.306 3726 Planarity : 0.005 0.044 3990 Dihedral : 7.490 55.282 4188 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 6.20 % Allowed : 17.32 % Favored : 76.48 % 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: -2.88 (0.14), residues: 2781 helix: -1.33 (0.19), residues: 645 sheet: -1.52 (0.21), residues: 525 loop : -2.37 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 110 HIS 0.005 0.001 HIS C 502 PHE 0.021 0.002 PHE A 513 TYR 0.020 0.002 TYR B 369 ARG 0.005 0.001 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 299 time to evaluate : 2.426 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 244 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9064 (tp) REVERT: A 253 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8630 (pt) REVERT: A 315 ARG cc_start: 0.6514 (mmm160) cc_final: 0.6279 (mmm160) REVERT: A 370 GLU cc_start: 0.6822 (pt0) cc_final: 0.6343 (pt0) REVERT: A 620 ASP cc_start: 0.8468 (t70) cc_final: 0.8206 (t0) REVERT: A 633 SER cc_start: 0.8898 (t) cc_final: 0.8590 (p) REVERT: A 770 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8261 (mt) REVERT: B 251 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: B 269 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 301 ASN cc_start: 0.8545 (m-40) cc_final: 0.8190 (m-40) REVERT: B 331 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8297 (t) REVERT: B 468 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9230 (mt) REVERT: B 494 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7502 (t80) REVERT: B 498 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8097 (pt) REVERT: C 210 ARG cc_start: 0.6311 (pmm-80) cc_final: 0.5565 (ptp-170) REVERT: C 269 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8234 (tp) REVERT: C 564 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8537 (ptt90) REVERT: C 874 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8191 (t160) outliers start: 151 outliers final: 96 residues processed: 414 average time/residue: 0.2876 time to fit residues: 196.4182 Evaluate side-chains 360 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 252 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 110 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 499 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain C residue 34 HIS Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 230 optimal weight: 0.0970 chunk 186 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 0.0870 chunk 242 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 overall best weight: 1.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS B 528 ASN B 880 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23229 Z= 0.239 Angle : 0.695 9.710 31620 Z= 0.347 Chirality : 0.046 0.258 3726 Planarity : 0.004 0.043 3990 Dihedral : 6.969 55.480 4187 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.20 % Allowed : 18.97 % Favored : 74.84 % 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: -2.57 (0.15), residues: 2781 helix: -0.99 (0.20), residues: 630 sheet: -1.34 (0.22), residues: 540 loop : -2.20 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 110 HIS 0.006 0.001 HIS B 552 PHE 0.024 0.002 PHE C 513 TYR 0.017 0.002 TYR C 369 ARG 0.004 0.000 ARG C 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 275 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8977 (tp) REVERT: A 253 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8533 (pt) REVERT: A 276 MET cc_start: 0.8257 (mmt) cc_final: 0.7695 (mmt) REVERT: A 315 ARG cc_start: 0.6487 (mmm160) cc_final: 0.6267 (mmm160) REVERT: A 367 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8534 (mtmt) REVERT: A 620 ASP cc_start: 0.8434 (t70) cc_final: 0.8216 (t0) REVERT: A 770 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8269 (mt) REVERT: A 852 ASN cc_start: 0.8788 (t160) cc_final: 0.8494 (t160) REVERT: B 210 ARG cc_start: 0.6075 (pmm-80) cc_final: 0.5606 (ptp-170) REVERT: B 269 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8108 (tp) REVERT: B 301 ASN cc_start: 0.8503 (m-40) cc_final: 0.8165 (m-40) REVERT: B 370 GLU cc_start: 0.7137 (pt0) cc_final: 0.6287 (pt0) REVERT: B 494 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: B 498 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8180 (pt) REVERT: C 210 ARG cc_start: 0.6209 (pmm-80) cc_final: 0.5562 (ptp-170) REVERT: C 269 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (tp) REVERT: C 494 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: C 564 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8619 (ptt90) REVERT: C 874 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8145 (t160) outliers start: 151 outliers final: 109 residues processed: 386 average time/residue: 0.2878 time to fit residues: 184.7766 Evaluate side-chains 365 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 246 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 528 ASN Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 585 MET Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 850 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 8.9990 chunk 242 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS B 528 ASN B 573 GLN B 880 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23229 Z= 0.180 Angle : 0.666 9.683 31620 Z= 0.333 Chirality : 0.045 0.249 3726 Planarity : 0.004 0.044 3990 Dihedral : 6.531 55.724 4184 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.87 % Allowed : 20.16 % Favored : 73.97 % 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: -2.41 (0.15), residues: 2781 helix: -0.84 (0.20), residues: 633 sheet: -1.22 (0.22), residues: 531 loop : -2.11 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 110 HIS 0.005 0.001 HIS B 552 PHE 0.025 0.001 PHE A 513 TYR 0.014 0.001 TYR C 369 ARG 0.004 0.000 ARG C 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 286 time to evaluate : 2.660 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 276 MET cc_start: 0.8237 (mmt) cc_final: 0.7726 (mmt) REVERT: A 315 ARG cc_start: 0.6461 (mmm160) cc_final: 0.6255 (mmm160) REVERT: A 367 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8500 (mtmt) REVERT: A 770 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8267 (mt) REVERT: B 210 ARG cc_start: 0.6060 (pmm-80) cc_final: 0.5597 (ptp-170) REVERT: B 217 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 251 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8484 (m-80) REVERT: B 301 ASN cc_start: 0.8508 (m-40) cc_final: 0.8224 (m-40) REVERT: B 370 GLU cc_start: 0.7148 (pt0) cc_final: 0.6552 (pt0) REVERT: B 494 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: B 564 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8458 (ptt90) REVERT: C 210 ARG cc_start: 0.6191 (pmm-80) cc_final: 0.5592 (ptp-170) REVERT: C 494 PHE cc_start: 0.8263 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: C 564 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8575 (ptt90) REVERT: C 599 VAL cc_start: 0.8468 (m) cc_final: 0.8263 (p) REVERT: C 874 ASN cc_start: 0.8603 (OUTLIER) cc_final: 0.8089 (t160) outliers start: 143 outliers final: 100 residues processed: 403 average time/residue: 0.2958 time to fit residues: 194.8043 Evaluate side-chains 352 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 244 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 723 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 163 optimal weight: 0.0980 chunk 124 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN C 118 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23229 Z= 0.233 Angle : 0.679 9.740 31620 Z= 0.339 Chirality : 0.046 0.249 3726 Planarity : 0.004 0.043 3990 Dihedral : 6.426 55.305 4184 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 6.73 % Allowed : 20.24 % Favored : 73.03 % 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: -2.28 (0.15), residues: 2781 helix: -0.69 (0.20), residues: 630 sheet: -1.20 (0.22), residues: 546 loop : -2.03 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 110 HIS 0.003 0.001 HIS B 552 PHE 0.028 0.002 PHE A 513 TYR 0.021 0.002 TYR A 414 ARG 0.007 0.000 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 256 time to evaluate : 2.407 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 244 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8967 (tp) REVERT: A 253 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8348 (pt) REVERT: A 276 MET cc_start: 0.8260 (mmt) cc_final: 0.7708 (mmt) REVERT: A 367 LYS cc_start: 0.8739 (mtmt) cc_final: 0.8521 (mtmt) REVERT: A 770 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8289 (mt) REVERT: A 950 ASP cc_start: 0.7604 (t70) cc_final: 0.7372 (t0) REVERT: B 210 ARG cc_start: 0.6086 (pmm-80) cc_final: 0.5625 (ptp-170) REVERT: B 251 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: B 269 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 301 ASN cc_start: 0.8523 (m-40) cc_final: 0.8251 (m-40) REVERT: B 336 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8375 (pp) REVERT: B 494 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: B 498 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8130 (pt) REVERT: B 564 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8459 (ptt90) REVERT: C 210 ARG cc_start: 0.6294 (pmm-80) cc_final: 0.5721 (ptp-170) REVERT: C 217 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (mp) REVERT: C 269 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8139 (tp) REVERT: C 564 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8617 (ptt90) REVERT: C 599 VAL cc_start: 0.8494 (m) cc_final: 0.8285 (p) REVERT: C 874 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8094 (t0) outliers start: 164 outliers final: 123 residues processed: 386 average time/residue: 0.2869 time to fit residues: 182.9326 Evaluate side-chains 372 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 236 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 852 ASN Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 578 GLU Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 852 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23229 Z= 0.247 Angle : 0.688 9.736 31620 Z= 0.344 Chirality : 0.046 0.248 3726 Planarity : 0.004 0.043 3990 Dihedral : 6.395 55.375 4182 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.77 % Allowed : 20.69 % Favored : 72.54 % 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: -2.25 (0.15), residues: 2781 helix: -0.63 (0.20), residues: 624 sheet: -1.20 (0.22), residues: 546 loop : -2.01 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 110 HIS 0.004 0.001 HIS C 918 PHE 0.025 0.002 PHE A 513 TYR 0.017 0.002 TYR C 369 ARG 0.006 0.000 ARG A 854 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 256 time to evaluate : 2.408 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 244 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 253 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8341 (pt) REVERT: A 276 MET cc_start: 0.8263 (mmt) cc_final: 0.7727 (mmt) REVERT: A 367 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8446 (mtmt) REVERT: A 370 GLU cc_start: 0.6931 (pt0) cc_final: 0.6721 (pt0) REVERT: A 770 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8291 (mt) REVERT: B 210 ARG cc_start: 0.6103 (pmm-80) cc_final: 0.5588 (ptp-170) REVERT: B 251 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: B 269 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8157 (tp) REVERT: B 301 ASN cc_start: 0.8502 (m-40) cc_final: 0.8277 (m-40) REVERT: B 336 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8312 (pp) REVERT: B 370 GLU cc_start: 0.7228 (pt0) cc_final: 0.6319 (pt0) REVERT: B 494 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7540 (t80) REVERT: B 498 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 564 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8461 (ptt90) REVERT: C 210 ARG cc_start: 0.6329 (pmm-80) cc_final: 0.5757 (ptp-170) REVERT: C 269 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8135 (tp) REVERT: C 564 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8621 (ptt90) REVERT: C 599 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8253 (p) REVERT: C 874 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8060 (t0) outliers start: 165 outliers final: 122 residues processed: 386 average time/residue: 0.2898 time to fit residues: 184.5137 Evaluate side-chains 374 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 239 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 578 GLU Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 850 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 226 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 249 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 528 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 880 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 HIS ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 GLN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS C 528 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23229 Z= 0.410 Angle : 0.781 11.165 31620 Z= 0.395 Chirality : 0.049 0.248 3726 Planarity : 0.005 0.046 3990 Dihedral : 6.938 54.641 4182 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 6.81 % Allowed : 21.10 % Favored : 72.09 % 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: -2.41 (0.15), residues: 2781 helix: -1.01 (0.19), residues: 666 sheet: -1.34 (0.22), residues: 540 loop : -2.00 (0.15), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 110 HIS 0.006 0.001 HIS B 319 PHE 0.033 0.002 PHE A 513 TYR 0.026 0.002 TYR C 369 ARG 0.006 0.001 ARG A 849 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 236 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9109 (tp) REVERT: A 253 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8585 (pt) REVERT: A 276 MET cc_start: 0.8324 (mmt) cc_final: 0.7758 (mmt) REVERT: A 770 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8351 (mt) REVERT: B 210 ARG cc_start: 0.6245 (pmm-80) cc_final: 0.5524 (ptp-170) REVERT: B 251 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8471 (m-80) REVERT: B 269 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8214 (tp) REVERT: B 370 GLU cc_start: 0.7286 (pt0) cc_final: 0.6412 (pt0) REVERT: B 494 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7584 (t80) REVERT: B 498 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8147 (pt) REVERT: B 564 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8491 (ptt90) REVERT: C 101 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7172 (m-70) REVERT: C 269 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (tp) REVERT: C 336 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8336 (pp) REVERT: C 367 LYS cc_start: 0.8476 (mtmt) cc_final: 0.8242 (pttt) REVERT: C 528 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8368 (p0) REVERT: C 564 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (ptt90) REVERT: C 582 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: C 874 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8236 (t160) outliers start: 166 outliers final: 133 residues processed: 371 average time/residue: 0.2955 time to fit residues: 180.6358 Evaluate side-chains 371 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 223 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 869 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 528 ASN Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 582 GLN Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 869 ILE Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 8.9990 chunk 161 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 277 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 221 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 175 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 23229 Z= 0.293 Angle : 0.733 10.801 31620 Z= 0.367 Chirality : 0.047 0.247 3726 Planarity : 0.004 0.046 3990 Dihedral : 6.831 55.394 4182 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.87 % Allowed : 22.41 % Favored : 71.72 % 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: -2.29 (0.15), residues: 2781 helix: -0.77 (0.20), residues: 636 sheet: -1.29 (0.22), residues: 540 loop : -1.96 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 110 HIS 0.004 0.001 HIS C 918 PHE 0.032 0.002 PHE A 513 TYR 0.021 0.002 TYR B 865 ARG 0.006 0.000 ARG A 849 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 241 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9041 (tp) REVERT: A 253 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8560 (pt) REVERT: A 276 MET cc_start: 0.8331 (mmt) cc_final: 0.7752 (mmt) REVERT: A 770 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8286 (mt) REVERT: B 210 ARG cc_start: 0.6210 (pmm-80) cc_final: 0.5502 (ptp-170) REVERT: B 251 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8377 (m-80) REVERT: B 269 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8177 (tp) REVERT: B 370 GLU cc_start: 0.7220 (pt0) cc_final: 0.6493 (pt0) REVERT: B 392 VAL cc_start: 0.5513 (OUTLIER) cc_final: 0.5288 (p) REVERT: B 494 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7546 (t80) REVERT: B 498 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8059 (pt) REVERT: B 564 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8489 (ptt90) REVERT: C 101 HIS cc_start: 0.7350 (OUTLIER) cc_final: 0.7023 (m-70) REVERT: C 269 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8235 (tp) REVERT: C 336 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8266 (pp) REVERT: C 367 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8220 (pttt) REVERT: C 564 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8582 (ptt90) REVERT: C 599 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 874 ASN cc_start: 0.8637 (OUTLIER) cc_final: 0.8189 (t160) outliers start: 143 outliers final: 121 residues processed: 358 average time/residue: 0.2888 time to fit residues: 170.2771 Evaluate side-chains 365 residues out of total 2436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 229 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 ASN Chi-restraints excluded: chain A residue 603 CYS Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain B residue 34 HIS Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 ARG Chi-restraints excluded: chain B residue 578 GLU Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 650 THR Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 348 VAL Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 360 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 413 THR Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 597 CYS Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 645 SER Chi-restraints excluded: chain C residue 650 THR Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 874 ASN Chi-restraints excluded: chain C residue 931 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.126799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103301 restraints weight = 39575.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104980 restraints weight = 23050.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106301 restraints weight = 15676.072| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 23229 Z= 0.284 Angle : 0.853 59.193 31620 Z= 0.455 Chirality : 0.049 1.017 3726 Planarity : 0.004 0.048 3990 Dihedral : 6.837 55.386 4182 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.35 % Favored : 90.61 % Rotamer: Outliers : 5.95 % Allowed : 22.62 % Favored : 71.43 % Cbeta Deviations : 0.04 % 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: -2.30 (0.15), residues: 2781 helix: -0.78 (0.20), residues: 636 sheet: -1.28 (0.22), residues: 540 loop : -1.98 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 110 HIS 0.004 0.001 HIS C 918 PHE 0.030 0.002 PHE A 513 TYR 0.019 0.002 TYR A 369 ARG 0.005 0.000 ARG A 849 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4368.44 seconds wall clock time: 80 minutes 17.67 seconds (4817.67 seconds total)