Starting phenix.real_space_refine on Sun Feb 18 14:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyd_30497/02_2024/7cyd_30497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyd_30497/02_2024/7cyd_30497.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/7cyd_30497/02_2024/7cyd_30497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyd_30497/02_2024/7cyd_30497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyd_30497/02_2024/7cyd_30497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cyd_30497/02_2024/7cyd_30497.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= 1.000 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 111 5.16 5 C 14052 2.51 5 N 3738 2.21 5 O 4419 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A GLU 1025": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 285": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 693": "OE1" <-> "OE2" Residue "B GLU 789": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B GLU 1025": "OE1" <-> "OE2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C GLU 285": "OE1" <-> "OE2" Residue "C GLU 650": "OE1" <-> "OE2" Residue "C GLU 693": "OE1" <-> "OE2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "C GLU 961": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1025": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22320 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 233 Chain: "B" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 233 Chain: "C" Number of atoms: 7122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 964, 7122 Classifications: {'peptide': 964} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 33, 'TRANS': 930} Chain breaks: 4 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 543 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 233 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.53, per 1000 atoms: 0.56 Number of scatterers: 22320 At special positions: 0 Unit cell: (133, 133, 151.2, 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 111 16.00 O 4419 8.00 N 3738 7.00 C 14052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 320 " distance=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 396 " distance=2.02 Simple disulfide: pdb=" SG CYS A 608 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 715 " - pdb=" SG CYS A 726 " distance=2.02 Simple disulfide: pdb=" SG CYS A 917 " - pdb=" SG CYS A 928 " distance=2.04 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 396 " distance=2.02 Simple disulfide: pdb=" SG CYS B 608 " - pdb=" SG CYS B 630 " distance=2.04 Simple disulfide: pdb=" SG CYS B 715 " - pdb=" SG CYS B 726 " distance=2.02 Simple disulfide: pdb=" SG CYS B 917 " - pdb=" SG CYS B 928 " distance=2.04 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 317 " - pdb=" SG CYS C 320 " distance=2.04 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 396 " distance=2.02 Simple disulfide: pdb=" SG CYS C 608 " - pdb=" SG CYS C 630 " distance=2.04 Simple disulfide: pdb=" SG CYS C 715 " - pdb=" SG CYS C 726 " distance=2.02 Simple disulfide: pdb=" SG CYS C 917 " - pdb=" SG CYS C 928 " distance=2.04 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 Atom "HETATM21940 O5 NAG B1201 .*. O " rejected from bonding due to valence issues. Atom "HETATM21744 O5 NAG A1201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN F 4 " - " MAN F 5 " " MAN H 4 " - " MAN H 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " MAN D 6 " - " MAN D 7 " " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA H 3 " - " MAN H 4 " " MAN H 6 " - " MAN H 7 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA F 3 " - " MAN F 6 " " BMA H 3 " - " MAN H 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A1201 " - " ASN A 98 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 171 " " NAG A1204 " - " ASN A 220 " " NAG A1205 " - " ASN A 326 " " NAG A1206 " - " ASN A 518 " " NAG A1207 " - " ASN A 440 " " NAG A1208 " - " ASN A 663 " " NAG A1209 " - " ASN A 542 " " NAG A1210 " - " ASN A 568 " " NAG A1211 " - " ASN A 581 " " NAG A1212 " - " ASN A 587 " " NAG A1213 " - " ASN A 671 " " NAG A1214 " - " ASN A1015 " " NAG B1201 " - " ASN B 98 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 171 " " NAG B1204 " - " ASN B 220 " " NAG B1205 " - " ASN B 326 " " NAG B1206 " - " ASN B 518 " " NAG B1207 " - " ASN B 440 " " NAG B1208 " - " ASN B 663 " " NAG B1209 " - " ASN B 542 " " NAG B1210 " - " ASN B 568 " " NAG B1211 " - " ASN B 581 " " NAG B1212 " - " ASN B 587 " " NAG B1213 " - " ASN B 671 " " NAG B1214 " - " ASN B1015 " " NAG C1201 " - " ASN C 98 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 171 " " NAG C1204 " - " ASN C 220 " " NAG C1205 " - " ASN C 326 " " NAG C1206 " - " ASN C 518 " " NAG C1207 " - " ASN C 440 " " NAG C1208 " - " ASN C 663 " " NAG C1209 " - " ASN C 542 " " NAG C1210 " - " ASN C 568 " " NAG C1211 " - " ASN C 581 " " NAG C1212 " - " ASN C 587 " " NAG C1213 " - " ASN C 671 " " NAG C1214 " - " ASN C1015 " " NAG D 1 " - " ASN A 62 " " NAG E 1 " - " ASN A 243 " " NAG F 1 " - " ASN B 62 " " NAG G 1 " - " ASN B 243 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN C 243 " Time building additional restraints: 10.81 Conformation dependent library (CDL) restraints added in 4.6 seconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5394 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 25.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 607 through 614 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN A 625 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR A 626 " --> pdb=" O LEU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 652 Processing helix chain 'A' and resid 655 through 661 removed outlier: 4.102A pdb=" N THR A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 661 " --> pdb=" O LYS A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 690 through 699 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 723 through 732 Processing helix chain 'A' and resid 741 through 757 removed outlier: 4.124A pdb=" N ALA A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN A 774 " --> pdb=" O SER A 770 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 776 " --> pdb=" O ALA A 772 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL A 780 " --> pdb=" O ARG A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS A 792 " --> pdb=" O GLN A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 853 Processing helix chain 'A' and resid 861 through 869 Processing helix chain 'A' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.593A pdb=" N ASP A1007 " --> pdb=" O THR A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 Processing helix chain 'B' and resid 257 through 266 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR B 626 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 652 Processing helix chain 'B' and resid 655 through 661 removed outlier: 4.103A pdb=" N THR B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU B 661 " --> pdb=" O LYS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 723 through 732 Processing helix chain 'B' and resid 741 through 757 removed outlier: 4.123A pdb=" N ALA B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN B 774 " --> pdb=" O SER B 770 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL B 780 " --> pdb=" O ARG B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS B 792 " --> pdb=" O GLN B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 853 Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.594A pdb=" N ASP B1007 " --> pdb=" O THR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1030 Processing helix chain 'C' and resid 257 through 266 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 616 through 626 removed outlier: 3.919A pdb=" N GLN C 625 " --> pdb=" O GLU C 621 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR C 626 " --> pdb=" O LEU C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 652 Processing helix chain 'C' and resid 655 through 661 removed outlier: 4.103A pdb=" N THR C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 661 " --> pdb=" O LYS C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 690 through 699 Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 723 through 732 Processing helix chain 'C' and resid 741 through 757 removed outlier: 4.123A pdb=" N ALA C 757 " --> pdb=" O ILE C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 781 removed outlier: 3.982A pdb=" N GLN C 774 " --> pdb=" O SER C 770 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL C 780 " --> pdb=" O ARG C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 810 removed outlier: 4.152A pdb=" N LYS C 792 " --> pdb=" O GLN C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 853 Processing helix chain 'C' and resid 861 through 869 Processing helix chain 'C' and resid 870 through 915 removed outlier: 3.535A pdb=" N ASN C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.593A pdb=" N ASP C1007 " --> pdb=" O THR C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1030 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL A 70 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 244 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG A 72 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 242 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 74 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 240 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 238 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 234 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A 117 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE A 195 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL A 70 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL A 244 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG A 72 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A 242 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE A 74 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 240 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA A 238 " --> pdb=" O PRO A 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU A 234 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP A 239 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A 254 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 241 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN A 243 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE A 143 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE A 132 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU A 133 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE A 209 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN A 502 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 512 " --> pdb=" O VAL A 504 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU A 481 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR A 473 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 363 removed outlier: 3.684A pdb=" N SER A 361 " --> pdb=" O ASN A 403 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET A 398 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER A 414 " --> pdb=" O MET A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 380 through 381 removed outlier: 3.548A pdb=" N VAL A 380 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 546 through 550 Processing sheet with id=AB2, first strand: chain 'A' and resid 580 through 585 Processing sheet with id=AB3, first strand: chain 'A' and resid 593 through 598 removed outlier: 4.211A pdb=" N GLN A 593 " --> pdb=" O HIS A 949 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 949 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA A 940 " --> pdb=" O GLY A 944 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL A 946 " --> pdb=" O VAL A 938 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 938 " --> pdb=" O VAL A 946 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 948 " --> pdb=" O SER A 936 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A 936 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A 950 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 604 through 606 Processing sheet with id=AB5, first strand: chain 'B' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL B 70 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 244 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 72 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 242 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE B 74 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 240 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 238 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 234 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE B 117 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 195 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 81 removed outlier: 5.008A pdb=" N VAL B 70 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL B 244 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 72 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 242 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE B 74 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 240 " --> pdb=" O PHE B 74 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA B 238 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LEU B 234 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N ASP B 239 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N TYR B 254 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 241 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN B 243 " --> pdb=" O ALA B 250 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE B 143 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ILE B 132 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU B 133 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE B 209 " --> pdb=" O PHE B 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN B 502 " --> pdb=" O MET B 514 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY B 512 " --> pdb=" O VAL B 504 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU B 481 " --> pdb=" O ILE B 494 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 473 " --> pdb=" O LEU B 481 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.684A pdb=" N SER B 361 " --> pdb=" O ASN B 403 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET B 398 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 414 " --> pdb=" O MET B 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 380 through 381 removed outlier: 3.549A pdb=" N VAL B 380 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 546 through 550 Processing sheet with id=AC6, first strand: chain 'B' and resid 580 through 585 Processing sheet with id=AC7, first strand: chain 'B' and resid 593 through 598 removed outlier: 4.212A pdb=" N GLN B 593 " --> pdb=" O HIS B 949 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N HIS B 949 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 944 " --> pdb=" O ALA B 940 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ALA B 940 " --> pdb=" O GLY B 944 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 946 " --> pdb=" O VAL B 938 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL B 938 " --> pdb=" O VAL B 946 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU B 948 " --> pdb=" O SER B 936 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER B 936 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 950 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 604 through 606 Processing sheet with id=AC9, first strand: chain 'C' and resid 70 through 81 removed outlier: 5.007A pdb=" N VAL C 70 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 244 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG C 72 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 242 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE C 74 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 240 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 238 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 234 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE C 117 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 195 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 70 through 81 removed outlier: 5.007A pdb=" N VAL C 70 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL C 244 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG C 72 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 242 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE C 74 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 240 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 238 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU C 234 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASP C 239 " --> pdb=" O TYR C 254 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TYR C 254 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 241 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE C 252 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN C 243 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 177 through 182 removed outlier: 3.554A pdb=" N PHE C 143 " --> pdb=" O ILE C 132 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE C 132 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 133 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 200 through 201 removed outlier: 4.126A pdb=" N PHE C 209 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 274 through 278 removed outlier: 3.766A pdb=" N GLN C 502 " --> pdb=" O MET C 514 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY C 512 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 290 through 291 removed outlier: 6.358A pdb=" N LEU C 481 " --> pdb=" O ILE C 494 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR C 473 " --> pdb=" O LEU C 481 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 363 removed outlier: 3.685A pdb=" N SER C 361 " --> pdb=" O ASN C 403 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET C 398 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER C 414 " --> pdb=" O MET C 398 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 380 through 381 removed outlier: 3.548A pdb=" N VAL C 380 " --> pdb=" O GLY C 427 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 546 through 550 Processing sheet with id=AE1, first strand: chain 'C' and resid 580 through 585 Processing sheet with id=AE2, first strand: chain 'C' and resid 593 through 598 removed outlier: 4.212A pdb=" N GLN C 593 " --> pdb=" O HIS C 949 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 949 " --> pdb=" O GLN C 593 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 944 " --> pdb=" O ALA C 940 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ALA C 940 " --> pdb=" O GLY C 944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 946 " --> pdb=" O VAL C 938 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL C 938 " --> pdb=" O VAL C 946 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU C 948 " --> pdb=" O SER C 936 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 936 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 950 " --> pdb=" O ILE C 934 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 604 through 606 762 hydrogen bonds defined for protein. 2097 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: 8.73 Time building geometry restraints manager: 11.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6776 1.33 - 1.46: 5720 1.46 - 1.58: 10145 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 22782 Sorted by residual: bond pdb=" C MET C 439 " pdb=" N ASN C 440 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" C MET A 439 " pdb=" N ASN A 440 " ideal model delta sigma weight residual 1.332 1.471 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" C MET B 439 " pdb=" N ASN B 440 " ideal model delta sigma weight residual 1.332 1.470 -0.139 1.35e-02 5.49e+03 1.06e+02 bond pdb=" N LEU A 953 " pdb=" CA LEU A 953 " ideal model delta sigma weight residual 1.453 1.488 -0.034 8.30e-03 1.45e+04 1.72e+01 bond pdb=" N LEU C 953 " pdb=" CA LEU C 953 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 ... (remaining 22777 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.69: 625 106.69 - 113.56: 12005 113.56 - 120.43: 9010 120.43 - 127.31: 8865 127.31 - 134.18: 161 Bond angle restraints: 30666 Sorted by residual: angle pdb=" CA GLY C 93 " pdb=" C GLY C 93 " pdb=" O GLY C 93 " ideal model delta sigma weight residual 122.37 117.87 4.50 7.30e-01 1.88e+00 3.81e+01 angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" O GLY A 93 " ideal model delta sigma weight residual 122.37 118.00 4.37 7.30e-01 1.88e+00 3.58e+01 angle pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" O GLY B 93 " ideal model delta sigma weight residual 122.37 118.03 4.34 7.30e-01 1.88e+00 3.53e+01 angle pdb=" C PHE A 318 " pdb=" CA PHE A 318 " pdb=" CB PHE A 318 " ideal model delta sigma weight residual 110.88 102.86 8.02 1.57e+00 4.06e-01 2.61e+01 angle pdb=" C PHE B 318 " pdb=" CA PHE B 318 " pdb=" CB PHE B 318 " ideal model delta sigma weight residual 110.88 102.88 8.00 1.57e+00 4.06e-01 2.60e+01 ... (remaining 30661 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.48: 13552 24.48 - 48.96: 774 48.96 - 73.44: 164 73.44 - 97.92: 39 97.92 - 122.39: 60 Dihedral angle restraints: 14589 sinusoidal: 6174 harmonic: 8415 Sorted by residual: dihedral pdb=" CB CYS C 369 " pdb=" SG CYS C 369 " pdb=" SG CYS C 396 " pdb=" CB CYS C 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.21 57.79 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS B 369 " pdb=" SG CYS B 369 " pdb=" SG CYS B 396 " pdb=" CB CYS B 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.25 57.75 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CB CYS A 369 " pdb=" SG CYS A 369 " pdb=" SG CYS A 396 " pdb=" CB CYS A 396 " ideal model delta sinusoidal sigma weight residual 93.00 35.26 57.74 1 1.00e+01 1.00e-02 4.48e+01 ... (remaining 14586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 3187 0.190 - 0.380: 88 0.380 - 0.571: 5 0.571 - 0.761: 1 0.761 - 0.951: 7 Chirality restraints: 3288 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.53e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.51e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-02 2.50e+03 1.47e+02 ... (remaining 3285 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.300 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG G 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.300 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG E 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.300 2.00e-02 2.50e+03 2.52e-01 7.96e+02 pdb=" C7 NAG I 1 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.432 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.023 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 184 2.45 - 3.06: 17289 3.06 - 3.68: 34145 3.68 - 4.29: 47323 4.29 - 4.90: 73175 Nonbonded interactions: 172116 Sorted by model distance: nonbonded pdb=" CB SER C 245 " pdb=" O7 NAG I 2 " model vdw 1.838 3.440 nonbonded pdb=" CB SER A 245 " pdb=" O7 NAG E 2 " model vdw 1.903 3.440 nonbonded pdb=" OG SER C 245 " pdb=" O7 NAG I 2 " model vdw 1.958 2.440 nonbonded pdb=" OG SER A 245 " pdb=" O7 NAG E 2 " model vdw 1.993 2.440 nonbonded pdb=" CB SER B 245 " pdb=" O7 NAG G 2 " model vdw 2.032 3.440 ... (remaining 172111 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' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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: 0.330 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: 3.170 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 65.210 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 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 : 0.009 0.139 22782 Z= 0.585 Angle : 1.214 8.867 30666 Z= 0.734 Chirality : 0.087 0.951 3288 Planarity : 0.012 0.253 4020 Dihedral : 17.869 122.395 9141 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.56 % Favored : 94.34 % Rotamer: Outliers : 9.09 % Allowed : 9.27 % Favored : 81.64 % Cbeta Deviations : 0.56 % 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: -3.27 (0.13), residues: 2862 helix: -2.65 (0.14), residues: 651 sheet: -1.66 (0.23), residues: 483 loop : -2.19 (0.13), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B 404 HIS 0.026 0.005 HIS C 345 PHE 0.030 0.003 PHE C 373 TYR 0.027 0.003 TYR A 144 ARG 0.011 0.002 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 795 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8844 (t) cc_final: 0.8518 (t) REVERT: A 102 ARG cc_start: 0.7643 (mpt-90) cc_final: 0.7293 (ttp-170) REVERT: A 129 ARG cc_start: 0.7488 (ptm160) cc_final: 0.7241 (ptm160) REVERT: A 192 GLU cc_start: 0.7701 (tt0) cc_final: 0.7243 (tt0) REVERT: A 202 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: A 371 PHE cc_start: 0.7557 (p90) cc_final: 0.6942 (p90) REVERT: A 375 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7895 (mtmt) REVERT: A 396 CYS cc_start: 0.4177 (p) cc_final: 0.3150 (p) REVERT: A 403 ASN cc_start: 0.7595 (t0) cc_final: 0.7285 (t0) REVERT: A 479 ASN cc_start: 0.8054 (m110) cc_final: 0.7851 (m110) REVERT: A 638 ARG cc_start: 0.9071 (ttp-110) cc_final: 0.8861 (ttp-110) REVERT: A 642 MET cc_start: 0.9027 (mtm) cc_final: 0.8787 (mtp) REVERT: A 643 LEU cc_start: 0.9248 (mt) cc_final: 0.9036 (mt) REVERT: A 650 GLU cc_start: 0.8621 (tp30) cc_final: 0.8172 (tp30) REVERT: A 652 LEU cc_start: 0.7436 (mt) cc_final: 0.7143 (mt) REVERT: A 669 ASP cc_start: 0.7858 (t0) cc_final: 0.7488 (t0) REVERT: A 672 LEU cc_start: 0.8873 (mt) cc_final: 0.8673 (mt) REVERT: A 693 GLU cc_start: 0.7729 (pt0) cc_final: 0.6981 (pp20) REVERT: A 723 ASP cc_start: 0.8003 (t0) cc_final: 0.7728 (t0) REVERT: A 747 MET cc_start: 0.8805 (mtm) cc_final: 0.8563 (mtp) REVERT: A 824 GLN cc_start: 0.8768 (mp10) cc_final: 0.8021 (mp10) REVERT: A 846 HIS cc_start: 0.8932 (t70) cc_final: 0.8631 (t-90) REVERT: A 850 GLN cc_start: 0.8866 (mt0) cc_final: 0.8230 (mt0) REVERT: A 853 GLN cc_start: 0.8636 (pp30) cc_final: 0.8130 (pp30) REVERT: A 854 ASN cc_start: 0.8322 (p0) cc_final: 0.7800 (p0) REVERT: A 855 PHE cc_start: 0.9207 (m-80) cc_final: 0.8987 (m-80) REVERT: A 856 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8419 (tp-100) REVERT: A 876 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 908 GLN cc_start: 0.8828 (mm110) cc_final: 0.8401 (mm110) REVERT: A 924 ARG cc_start: 0.9027 (mtp180) cc_final: 0.8482 (mtp-110) REVERT: A 936 SER cc_start: 0.7185 (t) cc_final: 0.6860 (t) REVERT: A 939 ASN cc_start: 0.8514 (t0) cc_final: 0.8237 (t0) REVERT: A 943 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7983 (tp30) REVERT: A 949 HIS cc_start: 0.7510 (m-70) cc_final: 0.6931 (m90) REVERT: A 991 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7233 (mmm-85) REVERT: B 156 HIS cc_start: 0.4095 (m90) cc_final: 0.3824 (m170) REVERT: B 192 GLU cc_start: 0.6489 (tt0) cc_final: 0.5801 (tt0) REVERT: B 387 PHE cc_start: 0.7522 (m-80) cc_final: 0.7224 (m-80) REVERT: B 506 TYR cc_start: 0.9332 (t80) cc_final: 0.9072 (t80) REVERT: B 519 PHE cc_start: 0.7715 (t80) cc_final: 0.7370 (t80) REVERT: B 567 ARG cc_start: 0.7683 (ttt180) cc_final: 0.7188 (ptt90) REVERT: B 595 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7566 (mp0) REVERT: B 621 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8275 (mt-10) REVERT: B 622 LEU cc_start: 0.9069 (mp) cc_final: 0.8857 (mp) REVERT: B 669 ASP cc_start: 0.7728 (t0) cc_final: 0.7489 (t0) REVERT: B 693 GLU cc_start: 0.7824 (pt0) cc_final: 0.7600 (pt0) REVERT: B 723 ASP cc_start: 0.8371 (t0) cc_final: 0.8047 (t70) REVERT: B 824 GLN cc_start: 0.8725 (mp10) cc_final: 0.8412 (mp10) REVERT: B 840 GLN cc_start: 0.8999 (tt0) cc_final: 0.8700 (tp40) REVERT: B 863 GLN cc_start: 0.8628 (tp40) cc_final: 0.8369 (tp-100) REVERT: B 875 ASP cc_start: 0.9277 (m-30) cc_final: 0.9036 (m-30) REVERT: B 879 ASP cc_start: 0.9236 (p0) cc_final: 0.8955 (p0) REVERT: B 885 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8792 (mmt90) REVERT: B 924 ARG cc_start: 0.8571 (mtp180) cc_final: 0.8221 (mtp-110) REVERT: B 925 TYR cc_start: 0.7778 (p90) cc_final: 0.7542 (p90) REVERT: B 943 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7786 (tp30) REVERT: B 958 LYS cc_start: 0.8274 (tppt) cc_final: 0.8036 (tptm) REVERT: B 999 GLU cc_start: 0.8589 (tm-30) cc_final: 0.7954 (tm-30) REVERT: C 192 GLU cc_start: 0.5867 (tt0) cc_final: 0.4901 (tt0) REVERT: C 202 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: C 264 CYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5672 (t) REVERT: C 349 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8127 (mttt) REVERT: C 506 TYR cc_start: 0.9278 (t80) cc_final: 0.9050 (t80) REVERT: C 588 TRP cc_start: 0.6994 (t-100) cc_final: 0.6535 (t-100) REVERT: C 597 LEU cc_start: 0.7855 (mt) cc_final: 0.7515 (mp) REVERT: C 613 CYS cc_start: 0.6983 (m) cc_final: 0.5491 (m) REVERT: C 616 ASN cc_start: 0.7257 (m-40) cc_final: 0.6612 (m-40) REVERT: C 619 CYS cc_start: 0.8576 (t) cc_final: 0.8238 (t) REVERT: C 642 MET cc_start: 0.9016 (mtm) cc_final: 0.8642 (mtp) REVERT: C 643 LEU cc_start: 0.9092 (mt) cc_final: 0.8673 (mt) REVERT: C 652 LEU cc_start: 0.7917 (mt) cc_final: 0.7678 (mt) REVERT: C 655 ASP cc_start: 0.8162 (m-30) cc_final: 0.7866 (t0) REVERT: C 824 GLN cc_start: 0.8390 (mp10) cc_final: 0.8119 (mp10) REVERT: C 850 GLN cc_start: 0.8995 (mt0) cc_final: 0.8778 (mt0) REVERT: C 863 GLN cc_start: 0.8596 (tp40) cc_final: 0.8189 (tp-100) REVERT: C 880 ARG cc_start: 0.7388 (ptp-170) cc_final: 0.7041 (ttm110) REVERT: C 885 ARG cc_start: 0.8911 (mtt180) cc_final: 0.8228 (mmt90) REVERT: C 912 GLN cc_start: 0.9086 (tt0) cc_final: 0.8381 (tp-100) REVERT: C 924 ARG cc_start: 0.9161 (mtp180) cc_final: 0.8773 (mtm-85) REVERT: C 999 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 1001 ARG cc_start: 0.8880 (ttm170) cc_final: 0.8445 (ttm-80) outliers start: 199 outliers final: 165 residues processed: 946 average time/residue: 0.3380 time to fit residues: 484.7676 Evaluate side-chains 848 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 680 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 446 CYS Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 320 CYS Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 446 CYS Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 946 VAL Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 264 CYS Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 317 CYS Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 446 CYS Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 575 SER Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 606 VAL Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 779 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 914 VAL Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1016 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN A 498 ASN A 834 GLN A 839 GLN A 863 GLN A 912 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 834 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 HIS ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 368 ASN C 507 GLN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 877 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22782 Z= 0.265 Angle : 0.818 11.041 30666 Z= 0.414 Chirality : 0.055 0.438 3288 Planarity : 0.005 0.060 4020 Dihedral : 13.940 99.319 4834 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.18 % Rotamer: Outliers : 6.67 % Allowed : 16.89 % Favored : 76.44 % 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: -2.53 (0.14), residues: 2862 helix: -0.83 (0.17), residues: 657 sheet: -1.64 (0.21), residues: 534 loop : -2.11 (0.13), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 404 HIS 0.010 0.003 HIS C 345 PHE 0.034 0.003 PHE A 697 TYR 0.027 0.002 TYR C 729 ARG 0.012 0.001 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 698 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 GLU cc_start: 0.8166 (tt0) cc_final: 0.7578 (tt0) REVERT: A 403 ASN cc_start: 0.7838 (t0) cc_final: 0.7502 (t0) REVERT: A 439 MET cc_start: 0.8645 (mtp) cc_final: 0.8117 (mtp) REVERT: A 479 ASN cc_start: 0.8191 (m110) cc_final: 0.7989 (m110) REVERT: A 621 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8529 (mm-30) REVERT: A 638 ARG cc_start: 0.9188 (ttp-110) cc_final: 0.8868 (ttp-110) REVERT: A 650 GLU cc_start: 0.8733 (tp30) cc_final: 0.8094 (tp30) REVERT: A 652 LEU cc_start: 0.7541 (mt) cc_final: 0.6997 (mt) REVERT: A 719 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5345 (tt) REVERT: A 747 MET cc_start: 0.8822 (mtm) cc_final: 0.8542 (mtp) REVERT: A 779 TYR cc_start: 0.8545 (t80) cc_final: 0.8133 (t80) REVERT: A 824 GLN cc_start: 0.8793 (mp10) cc_final: 0.8532 (mp10) REVERT: A 846 HIS cc_start: 0.8976 (t70) cc_final: 0.8743 (t-90) REVERT: A 850 GLN cc_start: 0.8712 (mt0) cc_final: 0.8330 (mt0) REVERT: A 853 GLN cc_start: 0.8757 (pp30) cc_final: 0.8211 (pp30) REVERT: A 854 ASN cc_start: 0.8567 (p0) cc_final: 0.8121 (p0) REVERT: A 855 PHE cc_start: 0.9212 (m-80) cc_final: 0.8968 (m-80) REVERT: A 856 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8379 (tp-100) REVERT: A 863 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8570 (tp-100) REVERT: A 876 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 904 ARG cc_start: 0.7938 (tpt-90) cc_final: 0.7088 (tpt170) REVERT: A 936 SER cc_start: 0.7158 (t) cc_final: 0.6746 (t) REVERT: A 939 ASN cc_start: 0.8337 (t0) cc_final: 0.7958 (t0) REVERT: A 943 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7816 (tp30) REVERT: A 949 HIS cc_start: 0.7373 (m-70) cc_final: 0.7030 (m-70) REVERT: B 192 GLU cc_start: 0.7468 (tt0) cc_final: 0.6731 (tt0) REVERT: B 207 ARG cc_start: 0.8277 (ptm160) cc_final: 0.7822 (tmm-80) REVERT: B 387 PHE cc_start: 0.7680 (m-80) cc_final: 0.7440 (m-80) REVERT: B 433 GLU cc_start: 0.5641 (pt0) cc_final: 0.5348 (pm20) REVERT: B 519 PHE cc_start: 0.7564 (t80) cc_final: 0.7064 (t80) REVERT: B 567 ARG cc_start: 0.7426 (ttt180) cc_final: 0.7106 (ptt90) REVERT: B 595 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 621 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8335 (mt-10) REVERT: B 635 ASP cc_start: 0.9291 (t70) cc_final: 0.8977 (t70) REVERT: B 669 ASP cc_start: 0.7619 (t0) cc_final: 0.7416 (t0) REVERT: B 840 GLN cc_start: 0.8848 (tt0) cc_final: 0.8607 (tp40) REVERT: B 870 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8144 (t0) REVERT: B 875 ASP cc_start: 0.9302 (m-30) cc_final: 0.8675 (m-30) REVERT: B 879 ASP cc_start: 0.9130 (p0) cc_final: 0.8876 (p0) REVERT: B 943 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7722 (tp30) REVERT: B 997 MET cc_start: 0.5589 (mmm) cc_final: 0.5361 (mmm) REVERT: C 59 LEU cc_start: 0.7514 (tt) cc_final: 0.7264 (tp) REVERT: C 207 ARG cc_start: 0.7701 (tmm-80) cc_final: 0.7119 (tmm-80) REVERT: C 349 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8117 (mttt) REVERT: C 409 TYR cc_start: 0.7831 (m-10) cc_final: 0.7625 (m-10) REVERT: C 616 ASN cc_start: 0.7735 (m-40) cc_final: 0.7392 (m-40) REVERT: C 619 CYS cc_start: 0.8687 (t) cc_final: 0.8342 (t) REVERT: C 638 ARG cc_start: 0.9193 (ttm110) cc_final: 0.8643 (ptm-80) REVERT: C 655 ASP cc_start: 0.8357 (m-30) cc_final: 0.7959 (t0) REVERT: C 789 GLU cc_start: 0.8814 (tp30) cc_final: 0.8392 (pt0) REVERT: C 824 GLN cc_start: 0.8485 (mp10) cc_final: 0.8184 (mp10) REVERT: C 839 GLN cc_start: 0.8715 (pt0) cc_final: 0.7965 (pt0) REVERT: C 863 GLN cc_start: 0.8597 (tp40) cc_final: 0.8331 (tp-100) REVERT: C 885 ARG cc_start: 0.8878 (mtt180) cc_final: 0.8604 (mmt90) REVERT: C 886 LEU cc_start: 0.9210 (mm) cc_final: 0.8910 (tp) REVERT: C 907 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8386 (ttp80) REVERT: C 908 GLN cc_start: 0.8857 (mm-40) cc_final: 0.7623 (mm-40) REVERT: C 924 ARG cc_start: 0.8879 (mtp180) cc_final: 0.8522 (mtm-85) REVERT: C 1001 ARG cc_start: 0.8852 (ttm170) cc_final: 0.8450 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7361 (m-80) cc_final: 0.7059 (m-80) outliers start: 146 outliers final: 120 residues processed: 792 average time/residue: 0.3521 time to fit residues: 419.6722 Evaluate side-chains 775 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 653 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 773 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 870 ASP Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1002 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 773 ILE Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 HIS A 912 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 HIS C 507 GLN C 731 ASN ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 846 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 GLN C 956 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 22782 Z= 0.512 Angle : 0.953 13.762 30666 Z= 0.483 Chirality : 0.058 0.429 3288 Planarity : 0.006 0.108 4020 Dihedral : 12.503 80.333 4742 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 29.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.35 % Favored : 91.54 % Rotamer: Outliers : 8.04 % Allowed : 20.50 % Favored : 71.46 % 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: -2.72 (0.14), residues: 2862 helix: -0.39 (0.18), residues: 657 sheet: -1.95 (0.21), residues: 492 loop : -2.44 (0.13), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP B 588 HIS 0.013 0.003 HIS B 345 PHE 0.038 0.004 PHE A 182 TYR 0.039 0.003 TYR C 729 ARG 0.010 0.001 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 696 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7940 (mpt-90) cc_final: 0.7432 (ttp-170) REVERT: A 104 ASP cc_start: 0.5403 (OUTLIER) cc_final: 0.5149 (p0) REVERT: A 192 GLU cc_start: 0.8357 (tt0) cc_final: 0.7648 (tt0) REVERT: A 349 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7422 (mtmm) REVERT: A 439 MET cc_start: 0.8801 (mtp) cc_final: 0.8327 (mtp) REVERT: A 445 LYS cc_start: 0.8328 (tptt) cc_final: 0.8094 (tptm) REVERT: A 567 ARG cc_start: 0.7626 (ttt180) cc_final: 0.6971 (ttt180) REVERT: A 595 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7799 (mt-10) REVERT: A 621 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 638 ARG cc_start: 0.9245 (ttp-110) cc_final: 0.8702 (ttp-110) REVERT: A 650 GLU cc_start: 0.8758 (tp30) cc_final: 0.8403 (tp30) REVERT: A 779 TYR cc_start: 0.8654 (t80) cc_final: 0.8257 (t80) REVERT: A 824 GLN cc_start: 0.8821 (mp10) cc_final: 0.8338 (mp10) REVERT: A 846 HIS cc_start: 0.8961 (t70) cc_final: 0.8714 (t-90) REVERT: A 850 GLN cc_start: 0.8889 (mt0) cc_final: 0.8407 (mt0) REVERT: A 853 GLN cc_start: 0.8995 (pp30) cc_final: 0.8329 (pp30) REVERT: A 854 ASN cc_start: 0.8621 (p0) cc_final: 0.8214 (p0) REVERT: A 856 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8356 (tp-100) REVERT: A 863 GLN cc_start: 0.8879 (tp-100) cc_final: 0.8587 (tp-100) REVERT: A 868 ARG cc_start: 0.8855 (mmp80) cc_final: 0.8607 (mmp80) REVERT: A 876 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7751 (tm-30) REVERT: A 877 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8855 (mm-40) REVERT: A 924 ARG cc_start: 0.9037 (ptp90) cc_final: 0.8396 (ttp-110) REVERT: A 925 TYR cc_start: 0.8202 (p90) cc_final: 0.7761 (p90) REVERT: A 939 ASN cc_start: 0.7982 (t0) cc_final: 0.7707 (t0) REVERT: A 953 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6036 (mt) REVERT: A 977 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8215 (tpp80) REVERT: A 978 GLN cc_start: 0.8103 (pm20) cc_final: 0.7865 (mp10) REVERT: A 997 MET cc_start: 0.4473 (tpt) cc_final: 0.4036 (tpt) REVERT: B 74 PHE cc_start: 0.8885 (m-80) cc_final: 0.8614 (m-80) REVERT: B 104 ASP cc_start: 0.5324 (OUTLIER) cc_final: 0.4901 (p0) REVERT: B 129 ARG cc_start: 0.7352 (ptm160) cc_final: 0.7143 (ptm160) REVERT: B 192 GLU cc_start: 0.7825 (tt0) cc_final: 0.6979 (tt0) REVERT: B 206 TYR cc_start: 0.8434 (p90) cc_final: 0.8232 (p90) REVERT: B 239 ASP cc_start: 0.8495 (t0) cc_final: 0.7922 (t0) REVERT: B 387 PHE cc_start: 0.7832 (m-80) cc_final: 0.7601 (m-80) REVERT: B 433 GLU cc_start: 0.6121 (pt0) cc_final: 0.5851 (pm20) REVERT: B 507 GLN cc_start: 0.8805 (mt0) cc_final: 0.8452 (mt0) REVERT: B 519 PHE cc_start: 0.7271 (t80) cc_final: 0.6841 (t80) REVERT: B 530 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8028 (mp) REVERT: B 567 ARG cc_start: 0.7246 (ttt180) cc_final: 0.6473 (ttt180) REVERT: B 621 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8568 (mt-10) REVERT: B 655 ASP cc_start: 0.7904 (t0) cc_final: 0.7675 (t0) REVERT: B 656 LYS cc_start: 0.8759 (tppt) cc_final: 0.8518 (tppt) REVERT: B 697 PHE cc_start: 0.8835 (m-80) cc_final: 0.8493 (m-80) REVERT: B 875 ASP cc_start: 0.9271 (m-30) cc_final: 0.9049 (m-30) REVERT: B 924 ARG cc_start: 0.8830 (mtp-110) cc_final: 0.8514 (ptp90) REVERT: B 943 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7217 (pt0) REVERT: B 958 LYS cc_start: 0.8726 (tppt) cc_final: 0.8386 (tptm) REVERT: C 207 ARG cc_start: 0.7663 (tmm-80) cc_final: 0.6843 (tmm-80) REVERT: C 349 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8171 (mttt) REVERT: C 398 MET cc_start: 0.7940 (mmm) cc_final: 0.7525 (mmm) REVERT: C 468 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7429 (tt) REVERT: C 567 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6939 (tpp-160) REVERT: C 597 LEU cc_start: 0.8050 (mt) cc_final: 0.7625 (mt) REVERT: C 616 ASN cc_start: 0.8448 (m-40) cc_final: 0.8190 (m-40) REVERT: C 619 CYS cc_start: 0.8694 (t) cc_final: 0.8284 (t) REVERT: C 697 PHE cc_start: 0.8980 (m-80) cc_final: 0.8667 (m-80) REVERT: C 782 LEU cc_start: 0.8324 (mp) cc_final: 0.7886 (mm) REVERT: C 824 GLN cc_start: 0.8595 (mp10) cc_final: 0.8302 (mp10) REVERT: C 863 GLN cc_start: 0.8453 (tp40) cc_final: 0.8146 (tp-100) REVERT: C 890 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9026 (p0) REVERT: C 912 GLN cc_start: 0.9046 (tt0) cc_final: 0.8842 (mt0) REVERT: C 924 ARG cc_start: 0.9017 (mtp180) cc_final: 0.8740 (mtm-85) REVERT: C 995 ARG cc_start: 0.8399 (tpp80) cc_final: 0.7951 (ttm-80) REVERT: C 1001 ARG cc_start: 0.8794 (ttm170) cc_final: 0.8418 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7546 (m-80) cc_final: 0.7213 (m-80) outliers start: 176 outliers final: 139 residues processed: 814 average time/residue: 0.3584 time to fit residues: 437.3152 Evaluate side-chains 813 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 668 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 264 CYS Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 918 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 720 SER Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 856 GLN Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 911 GLN Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 720 SER Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 922 SER Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1007 ASP Chi-restraints excluded: chain C residue 1016 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 262 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 249 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A 156 HIS ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN ** B 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 783 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22782 Z= 0.221 Angle : 0.795 14.236 30666 Z= 0.394 Chirality : 0.064 1.577 3288 Planarity : 0.005 0.048 4020 Dihedral : 11.068 67.694 4704 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.04 % Favored : 93.85 % Rotamer: Outliers : 6.44 % Allowed : 25.02 % Favored : 68.54 % 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: -2.43 (0.14), residues: 2862 helix: -0.00 (0.19), residues: 651 sheet: -1.69 (0.20), residues: 597 loop : -2.34 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 588 HIS 0.010 0.002 HIS B 345 PHE 0.025 0.002 PHE C 519 TYR 0.038 0.002 TYR A 206 ARG 0.007 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 686 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ARG cc_start: 0.7935 (mpt-90) cc_final: 0.7401 (ttp-170) REVERT: A 104 ASP cc_start: 0.5062 (OUTLIER) cc_final: 0.4807 (p0) REVERT: A 113 LEU cc_start: 0.4450 (OUTLIER) cc_final: 0.4002 (mt) REVERT: A 192 GLU cc_start: 0.8218 (tt0) cc_final: 0.7449 (tt0) REVERT: A 349 LYS cc_start: 0.7910 (mtmt) cc_final: 0.7417 (mtmm) REVERT: A 403 ASN cc_start: 0.8005 (t0) cc_final: 0.7763 (t0) REVERT: A 419 TRP cc_start: 0.8711 (OUTLIER) cc_final: 0.8482 (p90) REVERT: A 439 MET cc_start: 0.8786 (mtp) cc_final: 0.8196 (mtp) REVERT: A 445 LYS cc_start: 0.8294 (tptt) cc_final: 0.8026 (tptm) REVERT: A 515 LEU cc_start: 0.7733 (tp) cc_final: 0.7411 (tt) REVERT: A 621 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 650 GLU cc_start: 0.8795 (tp30) cc_final: 0.8303 (tp30) REVERT: A 669 ASP cc_start: 0.8139 (t0) cc_final: 0.7930 (t0) REVERT: A 719 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5089 (tt) REVERT: A 779 TYR cc_start: 0.8567 (t80) cc_final: 0.8282 (t80) REVERT: A 824 GLN cc_start: 0.8744 (mp10) cc_final: 0.8480 (mp10) REVERT: A 830 LEU cc_start: 0.9113 (mm) cc_final: 0.8909 (mm) REVERT: A 846 HIS cc_start: 0.8916 (t70) cc_final: 0.8608 (t-90) REVERT: A 850 GLN cc_start: 0.8803 (mt0) cc_final: 0.8484 (mt0) REVERT: A 852 ARG cc_start: 0.8846 (ttt-90) cc_final: 0.8444 (ttt-90) REVERT: A 854 ASN cc_start: 0.8733 (p0) cc_final: 0.8319 (p0) REVERT: A 856 GLN cc_start: 0.8683 (tp-100) cc_final: 0.8311 (tp-100) REVERT: A 863 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8806 (tp-100) REVERT: A 868 ARG cc_start: 0.8769 (mmp80) cc_final: 0.8516 (mmp80) REVERT: A 876 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 877 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8804 (mm-40) REVERT: A 924 ARG cc_start: 0.8977 (ptp90) cc_final: 0.8503 (ttp-110) REVERT: A 939 ASN cc_start: 0.7737 (t0) cc_final: 0.5862 (t0) REVERT: A 943 GLU cc_start: 0.7821 (tp30) cc_final: 0.7431 (tp30) REVERT: A 961 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 985 LYS cc_start: 0.8541 (tttt) cc_final: 0.8140 (tttp) REVERT: A 991 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8091 (tpp80) REVERT: A 997 MET cc_start: 0.4044 (tpt) cc_final: 0.3818 (tpt) REVERT: B 74 PHE cc_start: 0.8906 (m-80) cc_final: 0.8538 (m-80) REVERT: B 104 ASP cc_start: 0.4892 (OUTLIER) cc_final: 0.4354 (p0) REVERT: B 129 ARG cc_start: 0.7370 (ptm160) cc_final: 0.7141 (ptm160) REVERT: B 192 GLU cc_start: 0.8177 (tt0) cc_final: 0.7217 (tt0) REVERT: B 387 PHE cc_start: 0.7705 (m-80) cc_final: 0.7486 (m-80) REVERT: B 488 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8146 (mmmt) REVERT: B 506 TYR cc_start: 0.9221 (t80) cc_final: 0.8789 (t80) REVERT: B 507 GLN cc_start: 0.8777 (mt0) cc_final: 0.8444 (mt0) REVERT: B 519 PHE cc_start: 0.7427 (t80) cc_final: 0.6994 (t80) REVERT: B 567 ARG cc_start: 0.7341 (ttt180) cc_final: 0.6637 (ttt180) REVERT: B 595 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 621 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8329 (mt-10) REVERT: B 655 ASP cc_start: 0.8080 (t0) cc_final: 0.7807 (t0) REVERT: B 697 PHE cc_start: 0.8844 (m-80) cc_final: 0.8388 (m-80) REVERT: B 789 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8423 (tm-30) REVERT: B 879 ASP cc_start: 0.9057 (p0) cc_final: 0.8756 (p0) REVERT: B 889 LEU cc_start: 0.8924 (tp) cc_final: 0.8675 (tt) REVERT: B 911 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8582 (tm-30) REVERT: B 943 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7000 (pt0) REVERT: B 981 LEU cc_start: 0.6793 (tp) cc_final: 0.6591 (tp) REVERT: B 995 ARG cc_start: 0.8166 (ttm-80) cc_final: 0.7568 (ttm-80) REVERT: B 1032 GLU cc_start: 0.8244 (pp20) cc_final: 0.7907 (pp20) REVERT: C 207 ARG cc_start: 0.7675 (tmm-80) cc_final: 0.6973 (tmm-80) REVERT: C 305 TYR cc_start: 0.7324 (m-10) cc_final: 0.6827 (m-10) REVERT: C 349 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8030 (mttt) REVERT: C 468 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7379 (tt) REVERT: C 567 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7050 (tpp-160) REVERT: C 614 ASN cc_start: 0.9297 (t0) cc_final: 0.8985 (t0) REVERT: C 618 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7715 (tpp-160) REVERT: C 619 CYS cc_start: 0.8673 (t) cc_final: 0.8361 (t) REVERT: C 621 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7185 (mt-10) REVERT: C 635 ASP cc_start: 0.9413 (t0) cc_final: 0.9178 (t0) REVERT: C 638 ARG cc_start: 0.9283 (ttm110) cc_final: 0.8597 (ttp80) REVERT: C 642 MET cc_start: 0.8851 (mtp) cc_final: 0.8589 (mmm) REVERT: C 644 GLU cc_start: 0.8912 (pp20) cc_final: 0.8698 (pp20) REVERT: C 655 ASP cc_start: 0.7947 (t0) cc_final: 0.7744 (t0) REVERT: C 697 PHE cc_start: 0.8961 (m-80) cc_final: 0.8520 (m-80) REVERT: C 789 GLU cc_start: 0.8943 (tp30) cc_final: 0.8517 (pt0) REVERT: C 824 GLN cc_start: 0.8494 (mp10) cc_final: 0.8156 (mp10) REVERT: C 838 ASN cc_start: 0.9227 (m-40) cc_final: 0.9018 (p0) REVERT: C 863 GLN cc_start: 0.8451 (tp40) cc_final: 0.8216 (tp-100) REVERT: C 886 LEU cc_start: 0.9254 (mm) cc_final: 0.8901 (tp) REVERT: C 908 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8455 (mm-40) REVERT: C 924 ARG cc_start: 0.8865 (mtp180) cc_final: 0.8419 (ptp-110) REVERT: C 995 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8162 (ttm-80) REVERT: C 1001 ARG cc_start: 0.8715 (ttm170) cc_final: 0.8386 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7606 (m-80) cc_final: 0.7135 (m-80) outliers start: 141 outliers final: 109 residues processed: 776 average time/residue: 0.3544 time to fit residues: 412.5563 Evaluate side-chains 776 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 661 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 123 PHE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 733 ILE Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 830 LEU Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 763 SER Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 890 ASN Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 142 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN A 863 GLN ** A 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 GLN C 639 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 791 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22782 Z= 0.207 Angle : 0.747 12.960 30666 Z= 0.368 Chirality : 0.054 0.457 3288 Planarity : 0.004 0.048 4020 Dihedral : 9.997 59.950 4681 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.23 % Favored : 92.66 % Rotamer: Outliers : 6.39 % Allowed : 25.25 % Favored : 68.36 % 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: -2.37 (0.15), residues: 2862 helix: 0.03 (0.19), residues: 651 sheet: -1.57 (0.21), residues: 552 loop : -2.33 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 588 HIS 0.008 0.001 HIS B 345 PHE 0.044 0.002 PHE B1018 TYR 0.031 0.002 TYR A 748 ARG 0.009 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 673 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4815 (p0) REVERT: A 113 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4212 (mt) REVERT: A 192 GLU cc_start: 0.8386 (tt0) cc_final: 0.7700 (tt0) REVERT: A 349 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7275 (mtmm) REVERT: A 403 ASN cc_start: 0.8045 (t0) cc_final: 0.7797 (t0) REVERT: A 419 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.8202 (p90) REVERT: A 439 MET cc_start: 0.8816 (mtp) cc_final: 0.8076 (mtp) REVERT: A 445 LYS cc_start: 0.8325 (tptt) cc_final: 0.8034 (tptm) REVERT: A 514 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6291 (mtm) REVERT: A 515 LEU cc_start: 0.7792 (tp) cc_final: 0.7567 (tt) REVERT: A 582 LEU cc_start: 0.7884 (mt) cc_final: 0.7627 (mp) REVERT: A 621 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8012 (mm-30) REVERT: A 650 GLU cc_start: 0.8772 (tp30) cc_final: 0.7978 (tp30) REVERT: A 719 LEU cc_start: 0.5710 (OUTLIER) cc_final: 0.5150 (tt) REVERT: A 779 TYR cc_start: 0.8554 (t80) cc_final: 0.8303 (t80) REVERT: A 798 PHE cc_start: 0.8711 (t80) cc_final: 0.8050 (t80) REVERT: A 824 GLN cc_start: 0.8736 (mp10) cc_final: 0.8453 (mp10) REVERT: A 846 HIS cc_start: 0.8901 (t70) cc_final: 0.8595 (t-90) REVERT: A 850 GLN cc_start: 0.8863 (mt0) cc_final: 0.8512 (mt0) REVERT: A 854 ASN cc_start: 0.8769 (p0) cc_final: 0.8363 (p0) REVERT: A 856 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8306 (tp-100) REVERT: A 863 GLN cc_start: 0.9089 (tp40) cc_final: 0.8542 (tp-100) REVERT: A 876 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 877 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8825 (mm-40) REVERT: A 911 GLN cc_start: 0.8829 (pp30) cc_final: 0.8603 (pp30) REVERT: A 924 ARG cc_start: 0.9028 (ptp90) cc_final: 0.8015 (ptt90) REVERT: A 943 GLU cc_start: 0.7756 (tp30) cc_final: 0.7367 (tp30) REVERT: A 961 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7079 (tm-30) REVERT: A 985 LYS cc_start: 0.8547 (tttt) cc_final: 0.8167 (tttp) REVERT: A 991 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7882 (tpp80) REVERT: A 997 MET cc_start: 0.4173 (tpt) cc_final: 0.3841 (tpt) REVERT: B 104 ASP cc_start: 0.4820 (OUTLIER) cc_final: 0.4358 (p0) REVERT: B 129 ARG cc_start: 0.7371 (ptm160) cc_final: 0.7126 (ptm160) REVERT: B 192 GLU cc_start: 0.8089 (tt0) cc_final: 0.7189 (tt0) REVERT: B 207 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7721 (tmm-80) REVERT: B 387 PHE cc_start: 0.7734 (m-80) cc_final: 0.7502 (m-80) REVERT: B 439 MET cc_start: 0.8766 (mtp) cc_final: 0.8011 (mmm) REVERT: B 488 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8088 (mmmt) REVERT: B 506 TYR cc_start: 0.9183 (t80) cc_final: 0.8882 (t80) REVERT: B 507 GLN cc_start: 0.8775 (mt0) cc_final: 0.8472 (mt0) REVERT: B 519 PHE cc_start: 0.7340 (t80) cc_final: 0.6919 (t80) REVERT: B 567 ARG cc_start: 0.7303 (ttt180) cc_final: 0.6940 (ptm-80) REVERT: B 595 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 621 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8320 (mt-10) REVERT: B 655 ASP cc_start: 0.8109 (t0) cc_final: 0.7792 (t0) REVERT: B 697 PHE cc_start: 0.8856 (m-80) cc_final: 0.8187 (m-80) REVERT: B 870 ASP cc_start: 0.8275 (t0) cc_final: 0.7954 (t0) REVERT: B 877 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8613 (mm-40) REVERT: B 879 ASP cc_start: 0.8989 (p0) cc_final: 0.8674 (p0) REVERT: B 880 ARG cc_start: 0.8384 (ptp-110) cc_final: 0.8149 (ptp90) REVERT: B 889 LEU cc_start: 0.8949 (tp) cc_final: 0.8705 (tt) REVERT: B 911 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 943 GLU cc_start: 0.7948 (mm-30) cc_final: 0.6958 (pt0) REVERT: B 995 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7553 (ttm-80) REVERT: C 159 PHE cc_start: 0.6629 (m-80) cc_final: 0.6249 (m-80) REVERT: C 207 ARG cc_start: 0.7658 (tmm-80) cc_final: 0.7188 (tmm-80) REVERT: C 349 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8105 (mtmt) REVERT: C 445 LYS cc_start: 0.7972 (ttpt) cc_final: 0.7462 (tttm) REVERT: C 468 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7185 (tt) REVERT: C 567 ARG cc_start: 0.7486 (ttt180) cc_final: 0.7179 (tpp-160) REVERT: C 595 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 614 ASN cc_start: 0.9236 (t0) cc_final: 0.8970 (t0) REVERT: C 618 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7676 (tpp-160) REVERT: C 619 CYS cc_start: 0.8665 (t) cc_final: 0.8347 (t) REVERT: C 621 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7210 (mt-10) REVERT: C 638 ARG cc_start: 0.9293 (ttm110) cc_final: 0.8793 (ptm160) REVERT: C 642 MET cc_start: 0.8857 (mtp) cc_final: 0.8590 (mmm) REVERT: C 655 ASP cc_start: 0.7983 (t0) cc_final: 0.7668 (t0) REVERT: C 661 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.5878 (mt) REVERT: C 697 PHE cc_start: 0.8931 (m-80) cc_final: 0.8661 (m-80) REVERT: C 824 GLN cc_start: 0.8545 (mp10) cc_final: 0.8196 (mp10) REVERT: C 832 LYS cc_start: 0.9076 (ptmt) cc_final: 0.8854 (ptmt) REVERT: C 851 LEU cc_start: 0.9224 (tp) cc_final: 0.8991 (tp) REVERT: C 863 GLN cc_start: 0.8439 (tp40) cc_final: 0.8162 (tp-100) REVERT: C 911 GLN cc_start: 0.8443 (pp30) cc_final: 0.8087 (pp30) REVERT: C 995 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8191 (ttm-80) REVERT: C 1001 ARG cc_start: 0.8708 (ttm170) cc_final: 0.8367 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7418 (m-80) cc_final: 0.7126 (m-80) outliers start: 140 outliers final: 112 residues processed: 764 average time/residue: 0.3588 time to fit residues: 409.6161 Evaluate side-chains 781 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 661 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 625 GLN Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 913 LYS Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 6.9990 chunk 250 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 231 optimal weight: 0.0980 chunk 129 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 213 ASN A 246 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 783 GLN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22782 Z= 0.287 Angle : 0.777 12.776 30666 Z= 0.386 Chirality : 0.054 0.536 3288 Planarity : 0.004 0.051 4020 Dihedral : 9.590 59.898 4666 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.93 % Favored : 91.96 % Rotamer: Outliers : 7.21 % Allowed : 25.71 % Favored : 67.08 % 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: -2.40 (0.15), residues: 2862 helix: 0.05 (0.19), residues: 651 sheet: -1.68 (0.22), residues: 504 loop : -2.34 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 588 HIS 0.008 0.002 HIS B 345 PHE 0.045 0.002 PHE B1018 TYR 0.043 0.002 TYR A 206 ARG 0.017 0.001 ARG B 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 666 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8311 (ptm160) REVERT: A 104 ASP cc_start: 0.5310 (OUTLIER) cc_final: 0.5089 (p0) REVERT: A 113 LEU cc_start: 0.4235 (OUTLIER) cc_final: 0.3957 (mt) REVERT: A 192 GLU cc_start: 0.8424 (tt0) cc_final: 0.7704 (tt0) REVERT: A 349 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7287 (mtmm) REVERT: A 419 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.8199 (p90) REVERT: A 439 MET cc_start: 0.8789 (mtp) cc_final: 0.8460 (mtp) REVERT: A 445 LYS cc_start: 0.8425 (tptt) cc_final: 0.8196 (tptt) REVERT: A 530 LEU cc_start: 0.8789 (mp) cc_final: 0.8587 (mp) REVERT: A 567 ARG cc_start: 0.7640 (ttt180) cc_final: 0.7365 (ptt90) REVERT: A 621 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8242 (mm-30) REVERT: A 650 GLU cc_start: 0.8746 (tp30) cc_final: 0.8259 (tp30) REVERT: A 719 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5525 (tt) REVERT: A 779 TYR cc_start: 0.8623 (t80) cc_final: 0.8315 (t80) REVERT: A 824 GLN cc_start: 0.8718 (mp10) cc_final: 0.8432 (mp10) REVERT: A 834 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8412 (tp-100) REVERT: A 854 ASN cc_start: 0.8769 (p0) cc_final: 0.8390 (p0) REVERT: A 856 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8337 (tp-100) REVERT: A 863 GLN cc_start: 0.8999 (tp40) cc_final: 0.8487 (tp-100) REVERT: A 876 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7609 (tm-30) REVERT: A 877 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8838 (mm-40) REVERT: A 904 ARG cc_start: 0.7897 (tpt-90) cc_final: 0.7132 (tpp-160) REVERT: A 908 GLN cc_start: 0.8139 (mm110) cc_final: 0.7746 (mm-40) REVERT: A 961 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7092 (tm-30) REVERT: A 977 ARG cc_start: 0.8103 (tpp-160) cc_final: 0.7846 (tpp80) REVERT: A 985 LYS cc_start: 0.8621 (tttt) cc_final: 0.8222 (tttp) REVERT: A 991 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7877 (tpp80) REVERT: A 997 MET cc_start: 0.3988 (tpt) cc_final: 0.3619 (tpt) REVERT: B 104 ASP cc_start: 0.5043 (OUTLIER) cc_final: 0.4523 (p0) REVERT: B 129 ARG cc_start: 0.7254 (ptm160) cc_final: 0.6980 (ptm160) REVERT: B 192 GLU cc_start: 0.8114 (tt0) cc_final: 0.7352 (tt0) REVERT: B 387 PHE cc_start: 0.7756 (m-80) cc_final: 0.7525 (m-80) REVERT: B 439 MET cc_start: 0.8711 (mtp) cc_final: 0.7950 (mmm) REVERT: B 488 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8105 (mmmt) REVERT: B 506 TYR cc_start: 0.9152 (t80) cc_final: 0.8947 (t80) REVERT: B 507 GLN cc_start: 0.8806 (mt0) cc_final: 0.8542 (mt0) REVERT: B 519 PHE cc_start: 0.7410 (t80) cc_final: 0.6931 (t80) REVERT: B 567 ARG cc_start: 0.7353 (ttt180) cc_final: 0.6765 (ttt180) REVERT: B 595 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6837 (mt-10) REVERT: B 621 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8455 (mt-10) REVERT: B 655 ASP cc_start: 0.8050 (t0) cc_final: 0.7768 (t0) REVERT: B 697 PHE cc_start: 0.8882 (m-80) cc_final: 0.8252 (m-80) REVERT: B 728 GLN cc_start: 0.9137 (mt0) cc_final: 0.8853 (mt0) REVERT: B 789 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 870 ASP cc_start: 0.8295 (t0) cc_final: 0.7948 (t0) REVERT: B 879 ASP cc_start: 0.9012 (p0) cc_final: 0.8781 (p0) REVERT: B 880 ARG cc_start: 0.8417 (ptp-110) cc_final: 0.8188 (ptp90) REVERT: B 889 LEU cc_start: 0.8953 (tp) cc_final: 0.8717 (tt) REVERT: B 911 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8523 (tm-30) REVERT: B 924 ARG cc_start: 0.8615 (ptp90) cc_final: 0.8411 (ptp90) REVERT: B 943 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7009 (pt0) REVERT: B 958 LYS cc_start: 0.8676 (tptp) cc_final: 0.8264 (tptp) REVERT: B 981 LEU cc_start: 0.6941 (tp) cc_final: 0.6387 (tp) REVERT: B 995 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7557 (ttm-80) REVERT: C 102 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8424 (mmp80) REVERT: C 159 PHE cc_start: 0.6604 (m-80) cc_final: 0.6074 (m-10) REVERT: C 207 ARG cc_start: 0.7653 (tmm-80) cc_final: 0.7043 (tmm-80) REVERT: C 349 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8127 (mtmt) REVERT: C 468 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7316 (tt) REVERT: C 567 ARG cc_start: 0.7554 (ttt180) cc_final: 0.7253 (tpp-160) REVERT: C 595 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7284 (tm-30) REVERT: C 597 LEU cc_start: 0.7782 (mt) cc_final: 0.7426 (mt) REVERT: C 614 ASN cc_start: 0.9305 (t0) cc_final: 0.9062 (t0) REVERT: C 618 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7703 (tpp-160) REVERT: C 619 CYS cc_start: 0.8697 (t) cc_final: 0.8304 (t) REVERT: C 621 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 638 ARG cc_start: 0.9290 (ttm110) cc_final: 0.8760 (ptm160) REVERT: C 642 MET cc_start: 0.8895 (mtp) cc_final: 0.8622 (mmm) REVERT: C 655 ASP cc_start: 0.7896 (t0) cc_final: 0.7550 (t0) REVERT: C 697 PHE cc_start: 0.9095 (m-80) cc_final: 0.8621 (m-80) REVERT: C 824 GLN cc_start: 0.8542 (mp10) cc_final: 0.8176 (mp10) REVERT: C 838 ASN cc_start: 0.9220 (m-40) cc_final: 0.9003 (p0) REVERT: C 863 GLN cc_start: 0.8467 (tp40) cc_final: 0.8178 (tp-100) REVERT: C 904 ARG cc_start: 0.8532 (tpt170) cc_final: 0.8108 (tpt170) REVERT: C 995 ARG cc_start: 0.8464 (tpp80) cc_final: 0.8180 (ttm-80) REVERT: C 1001 ARG cc_start: 0.8727 (ttm170) cc_final: 0.8402 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7380 (m-80) cc_final: 0.7094 (m-80) outliers start: 158 outliers final: 137 residues processed: 769 average time/residue: 0.3624 time to fit residues: 417.0779 Evaluate side-chains 800 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 657 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 724 LEU Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 913 LYS Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 158 optimal weight: 0.7980 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 0.1980 chunk 155 optimal weight: 0.6980 chunk 277 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 GLN C 625 GLN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22782 Z= 0.191 Angle : 0.760 13.374 30666 Z= 0.371 Chirality : 0.053 0.515 3288 Planarity : 0.004 0.083 4020 Dihedral : 9.048 59.985 4666 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 6.12 % Allowed : 27.35 % Favored : 66.53 % 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: -2.35 (0.15), residues: 2862 helix: 0.02 (0.19), residues: 657 sheet: -1.62 (0.22), residues: 555 loop : -2.30 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 588 HIS 0.008 0.002 HIS C 345 PHE 0.027 0.002 PHE B1018 TYR 0.045 0.002 TYR A 206 ARG 0.009 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 670 time to evaluate : 2.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.5506 (OUTLIER) cc_final: 0.5175 (p0) REVERT: A 113 LEU cc_start: 0.3754 (OUTLIER) cc_final: 0.3376 (mt) REVERT: A 192 GLU cc_start: 0.8451 (tt0) cc_final: 0.7567 (tt0) REVERT: A 349 LYS cc_start: 0.7656 (mtmt) cc_final: 0.6918 (mtmm) REVERT: A 403 ASN cc_start: 0.8079 (t0) cc_final: 0.7814 (t0) REVERT: A 419 TRP cc_start: 0.8746 (OUTLIER) cc_final: 0.8025 (p90) REVERT: A 439 MET cc_start: 0.8806 (mtp) cc_final: 0.8140 (mtp) REVERT: A 445 LYS cc_start: 0.8463 (tptt) cc_final: 0.8219 (tptt) REVERT: A 514 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6356 (mtm) REVERT: A 515 LEU cc_start: 0.7540 (tp) cc_final: 0.7291 (tt) REVERT: A 567 ARG cc_start: 0.7677 (ttt180) cc_final: 0.7370 (ptt90) REVERT: A 621 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8176 (mm-30) REVERT: A 626 TYR cc_start: 0.8715 (m-10) cc_final: 0.8379 (m-10) REVERT: A 650 GLU cc_start: 0.8736 (tp30) cc_final: 0.7893 (tp30) REVERT: A 719 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5271 (tt) REVERT: A 779 TYR cc_start: 0.8531 (t80) cc_final: 0.8314 (t80) REVERT: A 824 GLN cc_start: 0.8672 (mp10) cc_final: 0.8361 (mp10) REVERT: A 832 LYS cc_start: 0.9185 (ttmm) cc_final: 0.8964 (ttmm) REVERT: A 834 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8426 (tp-100) REVERT: A 854 ASN cc_start: 0.8774 (p0) cc_final: 0.8395 (p0) REVERT: A 856 GLN cc_start: 0.8670 (tp-100) cc_final: 0.8310 (tp-100) REVERT: A 863 GLN cc_start: 0.8978 (tp40) cc_final: 0.8722 (tp-100) REVERT: A 876 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7597 (tm-30) REVERT: A 877 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8837 (mm-40) REVERT: A 904 ARG cc_start: 0.7881 (tpt-90) cc_final: 0.7675 (tpp-160) REVERT: A 924 ARG cc_start: 0.8785 (ptp90) cc_final: 0.7496 (ptt-90) REVERT: A 943 GLU cc_start: 0.7822 (tp30) cc_final: 0.7562 (tp30) REVERT: A 961 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7010 (tm-30) REVERT: A 991 ARG cc_start: 0.8217 (tpp80) cc_final: 0.7708 (tpp80) REVERT: A 997 MET cc_start: 0.3759 (tpt) cc_final: 0.3427 (tpt) REVERT: B 89 ARG cc_start: 0.5602 (mmt-90) cc_final: 0.5359 (mpt180) REVERT: B 104 ASP cc_start: 0.4957 (OUTLIER) cc_final: 0.4508 (p0) REVERT: B 129 ARG cc_start: 0.7289 (ptm160) cc_final: 0.6931 (ptm160) REVERT: B 192 GLU cc_start: 0.8168 (tt0) cc_final: 0.7475 (tt0) REVERT: B 387 PHE cc_start: 0.7727 (m-80) cc_final: 0.7485 (m-80) REVERT: B 439 MET cc_start: 0.8735 (mtp) cc_final: 0.8066 (mmm) REVERT: B 488 LYS cc_start: 0.8614 (mtmm) cc_final: 0.8012 (mmmt) REVERT: B 506 TYR cc_start: 0.9130 (t80) cc_final: 0.8877 (t80) REVERT: B 507 GLN cc_start: 0.8797 (mt0) cc_final: 0.8475 (mt0) REVERT: B 519 PHE cc_start: 0.7417 (t80) cc_final: 0.7019 (t80) REVERT: B 567 ARG cc_start: 0.7328 (ttt180) cc_final: 0.6946 (ptm-80) REVERT: B 601 SER cc_start: 0.9533 (m) cc_final: 0.8758 (p) REVERT: B 614 ASN cc_start: 0.9231 (t0) cc_final: 0.9012 (t0) REVERT: B 621 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8387 (mt-10) REVERT: B 624 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8279 (tptp) REVERT: B 655 ASP cc_start: 0.8116 (t0) cc_final: 0.7846 (t0) REVERT: B 697 PHE cc_start: 0.8963 (m-80) cc_final: 0.8278 (m-80) REVERT: B 728 GLN cc_start: 0.9054 (mt0) cc_final: 0.8792 (mt0) REVERT: B 779 TYR cc_start: 0.8434 (t80) cc_final: 0.8125 (t80) REVERT: B 840 GLN cc_start: 0.9272 (tp40) cc_final: 0.8518 (tt0) REVERT: B 870 ASP cc_start: 0.8165 (t0) cc_final: 0.7820 (t0) REVERT: B 879 ASP cc_start: 0.8992 (p0) cc_final: 0.8733 (p0) REVERT: B 889 LEU cc_start: 0.8875 (tp) cc_final: 0.8633 (tt) REVERT: B 943 GLU cc_start: 0.7908 (mm-30) cc_final: 0.6496 (pt0) REVERT: B 958 LYS cc_start: 0.8767 (tptp) cc_final: 0.8388 (tptp) REVERT: B 981 LEU cc_start: 0.7100 (tp) cc_final: 0.6581 (tp) REVERT: B 995 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7539 (ttm-80) REVERT: B 1026 LEU cc_start: 0.7872 (mp) cc_final: 0.7658 (mp) REVERT: B 1032 GLU cc_start: 0.8192 (pp20) cc_final: 0.7974 (pp20) REVERT: C 159 PHE cc_start: 0.6574 (m-80) cc_final: 0.6130 (m-10) REVERT: C 207 ARG cc_start: 0.7704 (tmm-80) cc_final: 0.7129 (tmm-80) REVERT: C 349 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8087 (mtmt) REVERT: C 398 MET cc_start: 0.7363 (mmm) cc_final: 0.6946 (mmm) REVERT: C 468 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7199 (tt) REVERT: C 567 ARG cc_start: 0.7530 (ttt180) cc_final: 0.7251 (tpp-160) REVERT: C 595 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7037 (tm-30) REVERT: C 597 LEU cc_start: 0.7706 (mt) cc_final: 0.7411 (mt) REVERT: C 614 ASN cc_start: 0.9220 (t0) cc_final: 0.8985 (t0) REVERT: C 618 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7660 (tpp-160) REVERT: C 619 CYS cc_start: 0.8717 (t) cc_final: 0.8324 (t) REVERT: C 621 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7471 (mt-10) REVERT: C 638 ARG cc_start: 0.9284 (ttm110) cc_final: 0.8870 (ttp80) REVERT: C 642 MET cc_start: 0.8949 (mtp) cc_final: 0.8592 (mmm) REVERT: C 655 ASP cc_start: 0.8019 (t0) cc_final: 0.7642 (t0) REVERT: C 661 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.5868 (mt) REVERT: C 697 PHE cc_start: 0.9085 (m-80) cc_final: 0.8567 (m-80) REVERT: C 824 GLN cc_start: 0.8594 (mp10) cc_final: 0.8194 (mp10) REVERT: C 863 GLN cc_start: 0.8465 (tp40) cc_final: 0.8013 (tp-100) REVERT: C 1001 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8326 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7203 (m-80) cc_final: 0.6951 (m-80) outliers start: 134 outliers final: 115 residues processed: 757 average time/residue: 0.3570 time to fit residues: 404.3224 Evaluate side-chains 775 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 652 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 712 TYR Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 913 LYS Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 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 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN A 978 GLN ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 956 GLN C 213 ASN ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22782 Z= 0.255 Angle : 0.780 12.599 30666 Z= 0.384 Chirality : 0.053 0.505 3288 Planarity : 0.004 0.055 4020 Dihedral : 8.885 59.918 4655 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.42 % Favored : 91.47 % Rotamer: Outliers : 6.39 % Allowed : 27.67 % Favored : 65.94 % 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: -2.40 (0.15), residues: 2862 helix: 0.09 (0.19), residues: 648 sheet: -1.71 (0.22), residues: 573 loop : -2.34 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP C 588 HIS 0.015 0.002 HIS A 895 PHE 0.028 0.002 PHE B 90 TYR 0.032 0.002 TYR A 748 ARG 0.010 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 666 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.5426 (OUTLIER) cc_final: 0.5116 (p0) REVERT: A 113 LEU cc_start: 0.3955 (OUTLIER) cc_final: 0.3722 (mt) REVERT: A 188 LYS cc_start: 0.8491 (tptt) cc_final: 0.8280 (pttt) REVERT: A 192 GLU cc_start: 0.8482 (tt0) cc_final: 0.7560 (tt0) REVERT: A 349 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7254 (mtmm) REVERT: A 419 TRP cc_start: 0.8731 (OUTLIER) cc_final: 0.8006 (p90) REVERT: A 439 MET cc_start: 0.8801 (mtp) cc_final: 0.8500 (mtp) REVERT: A 445 LYS cc_start: 0.8436 (tptt) cc_final: 0.8144 (tptt) REVERT: A 515 LEU cc_start: 0.7747 (tp) cc_final: 0.7370 (tt) REVERT: A 567 ARG cc_start: 0.7758 (ttt180) cc_final: 0.7398 (ptt90) REVERT: A 621 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8406 (mm-30) REVERT: A 626 TYR cc_start: 0.8729 (m-10) cc_final: 0.8330 (m-10) REVERT: A 650 GLU cc_start: 0.8722 (tp30) cc_final: 0.7886 (tp30) REVERT: A 719 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5016 (tt) REVERT: A 779 TYR cc_start: 0.8563 (t80) cc_final: 0.8310 (t80) REVERT: A 824 GLN cc_start: 0.8692 (mp10) cc_final: 0.8375 (mp10) REVERT: A 834 GLN cc_start: 0.8656 (tp-100) cc_final: 0.8412 (tp-100) REVERT: A 853 GLN cc_start: 0.9058 (pp30) cc_final: 0.8318 (pp30) REVERT: A 854 ASN cc_start: 0.8770 (p0) cc_final: 0.8520 (p0) REVERT: A 856 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8347 (tp-100) REVERT: A 863 GLN cc_start: 0.8997 (tp40) cc_final: 0.8388 (tm-30) REVERT: A 876 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7621 (tm-30) REVERT: A 877 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8838 (mm-40) REVERT: A 908 GLN cc_start: 0.8514 (mm110) cc_final: 0.8197 (mm-40) REVERT: A 943 GLU cc_start: 0.8048 (tp30) cc_final: 0.7549 (tp30) REVERT: A 961 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 985 LYS cc_start: 0.8644 (tttm) cc_final: 0.8239 (tptp) REVERT: A 997 MET cc_start: 0.3957 (tpt) cc_final: 0.3545 (tpt) REVERT: B 104 ASP cc_start: 0.5054 (OUTLIER) cc_final: 0.4555 (p0) REVERT: B 129 ARG cc_start: 0.7219 (ptm160) cc_final: 0.6887 (ptm160) REVERT: B 192 GLU cc_start: 0.8116 (tt0) cc_final: 0.7455 (tt0) REVERT: B 207 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7749 (tmm-80) REVERT: B 387 PHE cc_start: 0.7729 (m-80) cc_final: 0.7456 (m-80) REVERT: B 439 MET cc_start: 0.8716 (mtp) cc_final: 0.7940 (mmm) REVERT: B 467 PHE cc_start: 0.6191 (t80) cc_final: 0.5021 (t80) REVERT: B 488 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8247 (mmmt) REVERT: B 506 TYR cc_start: 0.9156 (t80) cc_final: 0.8926 (t80) REVERT: B 507 GLN cc_start: 0.8858 (mt0) cc_final: 0.8553 (mt0) REVERT: B 519 PHE cc_start: 0.7307 (t80) cc_final: 0.6928 (t80) REVERT: B 567 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6924 (ptm-80) REVERT: B 601 SER cc_start: 0.9531 (m) cc_final: 0.8845 (p) REVERT: B 614 ASN cc_start: 0.9223 (t0) cc_final: 0.8996 (t0) REVERT: B 621 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8529 (mt-10) REVERT: B 655 ASP cc_start: 0.8033 (t0) cc_final: 0.7708 (t0) REVERT: B 693 GLU cc_start: 0.7759 (pp20) cc_final: 0.6972 (pp20) REVERT: B 697 PHE cc_start: 0.9072 (m-80) cc_final: 0.8544 (m-80) REVERT: B 728 GLN cc_start: 0.9093 (mt0) cc_final: 0.8802 (mt0) REVERT: B 779 TYR cc_start: 0.8483 (t80) cc_final: 0.8125 (t80) REVERT: B 789 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 840 GLN cc_start: 0.9259 (tp40) cc_final: 0.8531 (tt0) REVERT: B 870 ASP cc_start: 0.8234 (t0) cc_final: 0.7864 (t0) REVERT: B 879 ASP cc_start: 0.8991 (p0) cc_final: 0.8734 (p0) REVERT: B 889 LEU cc_start: 0.8805 (tp) cc_final: 0.8591 (tt) REVERT: B 943 GLU cc_start: 0.7894 (mm-30) cc_final: 0.6473 (pt0) REVERT: B 981 LEU cc_start: 0.6946 (tp) cc_final: 0.6381 (tp) REVERT: B 995 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: B 1032 GLU cc_start: 0.8211 (pp20) cc_final: 0.8004 (pp20) REVERT: C 102 ARG cc_start: 0.8739 (mmp80) cc_final: 0.8486 (mmp80) REVERT: C 159 PHE cc_start: 0.6356 (m-80) cc_final: 0.5872 (m-10) REVERT: C 207 ARG cc_start: 0.7726 (tmm-80) cc_final: 0.7151 (tmm-80) REVERT: C 349 LYS cc_start: 0.8382 (mtmt) cc_final: 0.8098 (mtmt) REVERT: C 468 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7230 (tt) REVERT: C 530 LEU cc_start: 0.8714 (mp) cc_final: 0.8509 (mp) REVERT: C 567 ARG cc_start: 0.7544 (ttt180) cc_final: 0.7261 (tpp-160) REVERT: C 595 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 614 ASN cc_start: 0.9281 (t0) cc_final: 0.9052 (t0) REVERT: C 618 ARG cc_start: 0.8116 (mmm160) cc_final: 0.7741 (tpp-160) REVERT: C 619 CYS cc_start: 0.8703 (t) cc_final: 0.8304 (t) REVERT: C 621 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7538 (mt-10) REVERT: C 638 ARG cc_start: 0.9287 (ttm110) cc_final: 0.8565 (ttp80) REVERT: C 642 MET cc_start: 0.8992 (mtp) cc_final: 0.8626 (mmm) REVERT: C 655 ASP cc_start: 0.7930 (t0) cc_final: 0.7521 (t0) REVERT: C 661 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.5996 (mt) REVERT: C 693 GLU cc_start: 0.8662 (pt0) cc_final: 0.8340 (pt0) REVERT: C 697 PHE cc_start: 0.9034 (m-80) cc_final: 0.8622 (m-80) REVERT: C 824 GLN cc_start: 0.8585 (mp10) cc_final: 0.8148 (mp10) REVERT: C 863 GLN cc_start: 0.8446 (tp40) cc_final: 0.7989 (tp-100) REVERT: C 904 ARG cc_start: 0.8459 (tpt170) cc_final: 0.8093 (tpt170) REVERT: C 908 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8246 (mm-40) REVERT: C 1001 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8362 (ttm-80) outliers start: 140 outliers final: 125 residues processed: 764 average time/residue: 0.3634 time to fit residues: 416.3211 Evaluate side-chains 784 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 652 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 835 ASP Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 257 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 319 ASN C 639 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22782 Z= 0.273 Angle : 0.805 14.548 30666 Z= 0.397 Chirality : 0.054 0.495 3288 Planarity : 0.004 0.048 4020 Dihedral : 8.771 59.934 4647 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.70 % Favored : 91.19 % Rotamer: Outliers : 6.94 % Allowed : 27.58 % Favored : 65.48 % 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: -2.46 (0.15), residues: 2862 helix: 0.07 (0.19), residues: 648 sheet: -1.70 (0.22), residues: 570 loop : -2.42 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 588 HIS 0.019 0.002 HIS A 895 PHE 0.020 0.002 PHE B 90 TYR 0.047 0.002 TYR A 206 ARG 0.009 0.001 ARG B1001 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 665 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.4965 (p0) REVERT: A 113 LEU cc_start: 0.3797 (OUTLIER) cc_final: 0.3587 (mt) REVERT: A 188 LYS cc_start: 0.8585 (tptt) cc_final: 0.8304 (pttt) REVERT: A 192 GLU cc_start: 0.8248 (tt0) cc_final: 0.7366 (tt0) REVERT: A 282 GLN cc_start: 0.9239 (pm20) cc_final: 0.8410 (pp30) REVERT: A 349 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7357 (mtmm) REVERT: A 398 MET cc_start: 0.7448 (mmm) cc_final: 0.6803 (mmm) REVERT: A 419 TRP cc_start: 0.8754 (OUTLIER) cc_final: 0.7995 (p90) REVERT: A 439 MET cc_start: 0.8831 (mtp) cc_final: 0.8532 (mtp) REVERT: A 445 LYS cc_start: 0.8426 (tptt) cc_final: 0.8133 (tptt) REVERT: A 515 LEU cc_start: 0.7765 (tp) cc_final: 0.7383 (tt) REVERT: A 567 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7336 (ptt90) REVERT: A 621 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 626 TYR cc_start: 0.8731 (m-10) cc_final: 0.8323 (m-10) REVERT: A 650 GLU cc_start: 0.8725 (tp30) cc_final: 0.7902 (tp30) REVERT: A 719 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5063 (tt) REVERT: A 779 TYR cc_start: 0.8573 (t80) cc_final: 0.8332 (t80) REVERT: A 783 GLN cc_start: 0.7747 (pt0) cc_final: 0.7358 (pp30) REVERT: A 824 GLN cc_start: 0.8684 (mp10) cc_final: 0.8351 (mp10) REVERT: A 834 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8415 (tp-100) REVERT: A 853 GLN cc_start: 0.9036 (pp30) cc_final: 0.8293 (pp30) REVERT: A 854 ASN cc_start: 0.8776 (p0) cc_final: 0.8538 (p0) REVERT: A 856 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8366 (tp-100) REVERT: A 863 GLN cc_start: 0.9022 (tp40) cc_final: 0.8416 (tm-30) REVERT: A 876 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7762 (tm-30) REVERT: A 877 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8836 (mm-40) REVERT: A 908 GLN cc_start: 0.8538 (mm110) cc_final: 0.8209 (mm-40) REVERT: A 943 GLU cc_start: 0.8088 (tp30) cc_final: 0.7559 (tp30) REVERT: A 961 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 977 ARG cc_start: 0.8027 (tpp-160) cc_final: 0.7669 (tpp80) REVERT: A 985 LYS cc_start: 0.8454 (tttm) cc_final: 0.8119 (tptp) REVERT: A 997 MET cc_start: 0.3942 (tpt) cc_final: 0.3543 (tpt) REVERT: B 104 ASP cc_start: 0.4937 (OUTLIER) cc_final: 0.4351 (p0) REVERT: B 192 GLU cc_start: 0.8059 (tt0) cc_final: 0.7413 (tt0) REVERT: B 207 ARG cc_start: 0.7998 (ptm160) cc_final: 0.7691 (tmm-80) REVERT: B 387 PHE cc_start: 0.7685 (m-80) cc_final: 0.7426 (m-80) REVERT: B 439 MET cc_start: 0.8708 (mtp) cc_final: 0.7935 (mmm) REVERT: B 467 PHE cc_start: 0.6248 (t80) cc_final: 0.5257 (t80) REVERT: B 488 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8239 (mmmt) REVERT: B 506 TYR cc_start: 0.9156 (t80) cc_final: 0.8929 (t80) REVERT: B 507 GLN cc_start: 0.8833 (mt0) cc_final: 0.8569 (mt0) REVERT: B 519 PHE cc_start: 0.7200 (t80) cc_final: 0.6797 (t80) REVERT: B 530 LEU cc_start: 0.8136 (tt) cc_final: 0.7427 (mt) REVERT: B 567 ARG cc_start: 0.7289 (ttt180) cc_final: 0.6808 (ptm-80) REVERT: B 588 TRP cc_start: 0.6289 (t-100) cc_final: 0.6016 (t-100) REVERT: B 601 SER cc_start: 0.9535 (m) cc_final: 0.8846 (p) REVERT: B 614 ASN cc_start: 0.9249 (t0) cc_final: 0.9017 (t0) REVERT: B 621 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8509 (mt-10) REVERT: B 655 ASP cc_start: 0.8044 (t0) cc_final: 0.7698 (t0) REVERT: B 693 GLU cc_start: 0.7718 (pp20) cc_final: 0.6926 (pp20) REVERT: B 697 PHE cc_start: 0.9089 (m-80) cc_final: 0.8549 (m-80) REVERT: B 728 GLN cc_start: 0.9097 (mt0) cc_final: 0.8800 (mt0) REVERT: B 779 TYR cc_start: 0.8487 (t80) cc_final: 0.8118 (t80) REVERT: B 789 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 870 ASP cc_start: 0.8290 (t0) cc_final: 0.7920 (t0) REVERT: B 879 ASP cc_start: 0.8992 (p0) cc_final: 0.8739 (p0) REVERT: B 889 LEU cc_start: 0.8877 (tp) cc_final: 0.8666 (tt) REVERT: B 943 GLU cc_start: 0.7906 (mm-30) cc_final: 0.6677 (pt0) REVERT: B 995 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: B 1025 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: C 102 ARG cc_start: 0.8755 (mmp80) cc_final: 0.8524 (mmp80) REVERT: C 159 PHE cc_start: 0.6399 (m-80) cc_final: 0.5985 (m-10) REVERT: C 197 ARG cc_start: 0.8340 (ptp-110) cc_final: 0.8092 (ptp-110) REVERT: C 207 ARG cc_start: 0.7651 (tmm-80) cc_final: 0.6959 (tmm-80) REVERT: C 349 LYS cc_start: 0.8379 (mtmt) cc_final: 0.8093 (mttt) REVERT: C 468 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7340 (tt) REVERT: C 530 LEU cc_start: 0.8838 (mp) cc_final: 0.8638 (mp) REVERT: C 567 ARG cc_start: 0.7535 (ttt180) cc_final: 0.7265 (tpp-160) REVERT: C 595 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7592 (tm-30) REVERT: C 614 ASN cc_start: 0.9321 (t0) cc_final: 0.9011 (t0) REVERT: C 618 ARG cc_start: 0.8125 (mmm160) cc_final: 0.7736 (tpp-160) REVERT: C 619 CYS cc_start: 0.8626 (t) cc_final: 0.8194 (t) REVERT: C 621 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 638 ARG cc_start: 0.9282 (ttm110) cc_final: 0.8862 (ttp80) REVERT: C 642 MET cc_start: 0.8971 (mtp) cc_final: 0.8571 (mmm) REVERT: C 655 ASP cc_start: 0.7939 (t0) cc_final: 0.7504 (t0) REVERT: C 661 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.6070 (mt) REVERT: C 693 GLU cc_start: 0.8675 (pt0) cc_final: 0.8159 (pt0) REVERT: C 697 PHE cc_start: 0.9050 (m-80) cc_final: 0.8705 (m-80) REVERT: C 824 GLN cc_start: 0.8591 (mp10) cc_final: 0.8154 (mp10) REVERT: C 832 LYS cc_start: 0.9397 (pttt) cc_final: 0.9135 (pttt) REVERT: C 904 ARG cc_start: 0.8442 (tpt170) cc_final: 0.8183 (tpt170) REVERT: C 1001 ARG cc_start: 0.8691 (ttm170) cc_final: 0.8257 (ttm-80) outliers start: 152 outliers final: 139 residues processed: 768 average time/residue: 0.3678 time to fit residues: 422.7078 Evaluate side-chains 801 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 654 time to evaluate : 2.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 720 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 922 SER Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 638 ARG Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 724 LEU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1025 GLU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 319 ASN Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 342 ASP Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 553 PHE Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 798 PHE Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.9980 chunk 273 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 0.8980 chunk 228 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN C 319 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 GLN ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22782 Z= 0.196 Angle : 0.801 16.235 30666 Z= 0.392 Chirality : 0.054 0.506 3288 Planarity : 0.004 0.054 4020 Dihedral : 8.385 59.641 4647 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.79 % Favored : 92.10 % Rotamer: Outliers : 5.71 % Allowed : 28.63 % Favored : 65.66 % 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: -2.43 (0.15), residues: 2862 helix: 0.02 (0.19), residues: 648 sheet: -1.65 (0.23), residues: 513 loop : -2.37 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 588 HIS 0.020 0.002 HIS A 895 PHE 0.032 0.002 PHE B1018 TYR 0.046 0.001 TYR A 206 ARG 0.010 0.001 ARG B1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 674 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.5497 (OUTLIER) cc_final: 0.5128 (p0) REVERT: A 113 LEU cc_start: 0.3645 (OUTLIER) cc_final: 0.3444 (mt) REVERT: A 188 LYS cc_start: 0.8471 (tptt) cc_final: 0.8247 (pttt) REVERT: A 192 GLU cc_start: 0.8234 (tt0) cc_final: 0.7386 (tt0) REVERT: A 349 LYS cc_start: 0.7587 (mtmt) cc_final: 0.6938 (mtmm) REVERT: A 403 ASN cc_start: 0.8136 (t0) cc_final: 0.7846 (t0) REVERT: A 419 TRP cc_start: 0.8774 (OUTLIER) cc_final: 0.8152 (p90) REVERT: A 439 MET cc_start: 0.8840 (mtp) cc_final: 0.8560 (mtp) REVERT: A 445 LYS cc_start: 0.8466 (tptt) cc_final: 0.8160 (tptt) REVERT: A 514 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.6561 (mtm) REVERT: A 515 LEU cc_start: 0.7737 (tp) cc_final: 0.7385 (tt) REVERT: A 621 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 626 TYR cc_start: 0.8637 (m-10) cc_final: 0.8302 (m-10) REVERT: A 650 GLU cc_start: 0.8689 (tp30) cc_final: 0.7842 (tp30) REVERT: A 652 LEU cc_start: 0.7790 (mt) cc_final: 0.7172 (mt) REVERT: A 719 LEU cc_start: 0.5801 (OUTLIER) cc_final: 0.5313 (tt) REVERT: A 783 GLN cc_start: 0.7670 (pt0) cc_final: 0.7275 (pp30) REVERT: A 824 GLN cc_start: 0.8642 (mp10) cc_final: 0.8300 (mp10) REVERT: A 834 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8447 (tp-100) REVERT: A 853 GLN cc_start: 0.9020 (pp30) cc_final: 0.8266 (pp30) REVERT: A 854 ASN cc_start: 0.8772 (p0) cc_final: 0.8566 (p0) REVERT: A 856 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8343 (tp-100) REVERT: A 863 GLN cc_start: 0.9005 (tp40) cc_final: 0.8405 (tm-30) REVERT: A 876 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 877 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8832 (mm-40) REVERT: A 943 GLU cc_start: 0.7844 (tp30) cc_final: 0.7376 (tp30) REVERT: A 961 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7091 (tm-30) REVERT: A 997 MET cc_start: 0.3740 (tpt) cc_final: 0.3377 (tpt) REVERT: B 104 ASP cc_start: 0.5255 (OUTLIER) cc_final: 0.4784 (p0) REVERT: B 129 ARG cc_start: 0.7279 (ptm160) cc_final: 0.7066 (ptm160) REVERT: B 192 GLU cc_start: 0.8169 (tt0) cc_final: 0.7536 (tt0) REVERT: B 387 PHE cc_start: 0.7815 (m-80) cc_final: 0.7542 (m-80) REVERT: B 439 MET cc_start: 0.8712 (mtp) cc_final: 0.8005 (mmm) REVERT: B 488 LYS cc_start: 0.8691 (mtmm) cc_final: 0.8165 (mmmt) REVERT: B 506 TYR cc_start: 0.9120 (t80) cc_final: 0.8835 (t80) REVERT: B 507 GLN cc_start: 0.8841 (mt0) cc_final: 0.8542 (mt0) REVERT: B 519 PHE cc_start: 0.7200 (t80) cc_final: 0.6863 (t80) REVERT: B 533 PHE cc_start: 0.8065 (p90) cc_final: 0.7601 (p90) REVERT: B 567 ARG cc_start: 0.7269 (ttt180) cc_final: 0.6968 (ptm-80) REVERT: B 588 TRP cc_start: 0.6358 (t-100) cc_final: 0.6124 (t-100) REVERT: B 601 SER cc_start: 0.9540 (m) cc_final: 0.8793 (p) REVERT: B 614 ASN cc_start: 0.9202 (t0) cc_final: 0.8976 (t0) REVERT: B 621 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8483 (mt-10) REVERT: B 624 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8211 (tptm) REVERT: B 655 ASP cc_start: 0.8107 (t0) cc_final: 0.7811 (t0) REVERT: B 693 GLU cc_start: 0.7731 (pp20) cc_final: 0.6855 (pp20) REVERT: B 697 PHE cc_start: 0.9087 (m-80) cc_final: 0.8581 (m-80) REVERT: B 728 GLN cc_start: 0.9009 (mt0) cc_final: 0.8713 (mt0) REVERT: B 779 TYR cc_start: 0.8444 (t80) cc_final: 0.8139 (t80) REVERT: B 870 ASP cc_start: 0.8172 (t0) cc_final: 0.7777 (t0) REVERT: B 889 LEU cc_start: 0.8763 (tp) cc_final: 0.8549 (tt) REVERT: B 943 GLU cc_start: 0.7852 (mm-30) cc_final: 0.6728 (pt0) REVERT: B 995 ARG cc_start: 0.8190 (ttm-80) cc_final: 0.7569 (ttm-80) REVERT: C 159 PHE cc_start: 0.6486 (m-80) cc_final: 0.5904 (m-10) REVERT: C 197 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.8076 (ptp-110) REVERT: C 207 ARG cc_start: 0.7712 (tmm-80) cc_final: 0.7154 (tmm-80) REVERT: C 305 TYR cc_start: 0.7728 (m-10) cc_final: 0.7465 (m-10) REVERT: C 349 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8055 (mttt) REVERT: C 468 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7200 (tt) REVERT: C 530 LEU cc_start: 0.8874 (mp) cc_final: 0.8669 (mp) REVERT: C 567 ARG cc_start: 0.7525 (ttt180) cc_final: 0.7262 (tpp-160) REVERT: C 595 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7378 (tm-30) REVERT: C 618 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7825 (tpp-160) REVERT: C 619 CYS cc_start: 0.8643 (t) cc_final: 0.8237 (t) REVERT: C 621 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 638 ARG cc_start: 0.9283 (ttm110) cc_final: 0.8855 (ptm160) REVERT: C 642 MET cc_start: 0.8995 (mtp) cc_final: 0.8636 (mmm) REVERT: C 655 ASP cc_start: 0.7903 (t0) cc_final: 0.7446 (t0) REVERT: C 661 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5609 (mt) REVERT: C 693 GLU cc_start: 0.8646 (pt0) cc_final: 0.8337 (pt0) REVERT: C 697 PHE cc_start: 0.9091 (m-80) cc_final: 0.8639 (m-80) REVERT: C 789 GLU cc_start: 0.8855 (tp30) cc_final: 0.8361 (pt0) REVERT: C 824 GLN cc_start: 0.8552 (mp10) cc_final: 0.8115 (mp10) REVERT: C 832 LYS cc_start: 0.9263 (pttt) cc_final: 0.9009 (pttt) REVERT: C 856 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6535 (tm-30) REVERT: C 904 ARG cc_start: 0.8368 (tpt170) cc_final: 0.7491 (tpt170) REVERT: C 908 GLN cc_start: 0.8732 (mm-40) cc_final: 0.7977 (mm-40) REVERT: C 991 ARG cc_start: 0.8340 (mmt90) cc_final: 0.7177 (mmm-85) REVERT: C 1001 ARG cc_start: 0.8650 (ttm170) cc_final: 0.8431 (ttm-80) REVERT: C 1018 PHE cc_start: 0.7097 (m-80) cc_final: 0.6595 (m-80) outliers start: 125 outliers final: 113 residues processed: 762 average time/residue: 0.3497 time to fit residues: 399.5355 Evaluate side-chains 777 residues out of total 2505 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 656 time to evaluate : 2.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 518 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 604 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 CYS Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 676 ILE Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 712 TYR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 871 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 903 VAL Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 264 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 518 ASN Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 676 ILE Chi-restraints excluded: chain B residue 682 SER Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 701 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 891 VAL Chi-restraints excluded: chain B residue 903 VAL Chi-restraints excluded: chain B residue 904 ARG Chi-restraints excluded: chain B residue 925 TYR Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 327 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 479 ASN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 661 LEU Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 701 VAL Chi-restraints excluded: chain C residue 712 TYR Chi-restraints excluded: chain C residue 871 ILE Chi-restraints excluded: chain C residue 903 VAL Chi-restraints excluded: chain C residue 966 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1007 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 210 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 28 optimal weight: 0.0370 chunk 42 optimal weight: 10.0000 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 ASN C 614 ASN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 840 GLN ** C 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.126383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.115741 restraints weight = 56661.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.118338 restraints weight = 29643.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.120070 restraints weight = 18177.252| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22782 Z= 0.236 Angle : 0.812 15.214 30666 Z= 0.399 Chirality : 0.054 0.490 3288 Planarity : 0.004 0.058 4020 Dihedral : 8.341 59.581 4647 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.77 % Favored : 91.13 % Rotamer: Outliers : 6.39 % Allowed : 28.04 % Favored : 65.57 % 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: -2.46 (0.15), residues: 2862 helix: 0.06 (0.19), residues: 648 sheet: -1.71 (0.22), residues: 585 loop : -2.40 (0.14), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 588 HIS 0.019 0.002 HIS A 895 PHE 0.032 0.002 PHE B1018 TYR 0.030 0.002 TYR A 748 ARG 0.010 0.001 ARG B1001 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6558.73 seconds wall clock time: 118 minutes 13.65 seconds (7093.65 seconds total)