Starting phenix.real_space_refine on Tue Feb 20 08:48:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6i_23697/02_2024/7m6i_23697_neut.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 116 5.16 5 C 17397 2.51 5 N 4514 2.21 5 O 5332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27359 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7814 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 8 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7801 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "M" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 897 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.83, per 1000 atoms: 0.51 Number of scatterers: 27359 At special positions: 0 Unit cell: (131.219, 140.778, 196.394, 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 116 16.00 O 5332 8.00 N 4514 7.00 C 17397 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.06 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 "HETATM27007 O5 NAG A1301 .*. O " rejected from bonding due to valence issues. Atom "HETATM27119 O5 NAG A1309 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 717 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C 657 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN B 165 " " NAG F 1 " - " ASN B 709 " " NAG G 1 " - " ASN C 709 " " NAG I 1 " - " ASN C 165 " Time building additional restraints: 10.97 Conformation dependent library (CDL) restraints added in 5.1 seconds 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6422 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 51 sheets defined 23.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.272A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.551A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.746A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.833A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.691A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 967 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.504A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.219A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.959A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.991A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.764A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.753A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.889A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.492A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.422A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.754A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.625A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.244A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.866A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.660A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.702A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.809A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.769A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 4.100A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.447A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 10.457A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.900A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.965A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.869A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.685A pdb=" N ASN A 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.241A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.612A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.530A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.507A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.878A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 195 through 197 removed outlier: 6.897A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.535A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.570A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.730A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.173A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.269A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.813A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.813A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.630A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.608A pdb=" N HIS C 49 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.100A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.663A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.742A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.256A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.843A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.271A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.062A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.795A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.677A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL H 20 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET H 80 " --> pdb=" O VAL H 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.533A pdb=" N ILE H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN H 58 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 93 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL H 37 " --> pdb=" O TYR H 91 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.654A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.995A pdb=" N LEU L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 18 through 20 removed outlier: 3.786A pdb=" N VAL M 20 " --> pdb=" O MET M 80 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET M 80 " --> pdb=" O VAL M 20 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.552A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AF5, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.535A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 53 through 54 removed outlier: 7.099A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2706 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: 12.51 Time building geometry restraints manager: 11.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6971 1.33 - 1.46: 8179 1.46 - 1.59: 12663 1.59 - 1.72: 0 1.72 - 1.85: 145 Bond restraints: 27958 Sorted by residual: bond pdb=" N TYR A 473 " pdb=" CA TYR A 473 " ideal model delta sigma weight residual 1.457 1.490 -0.033 6.40e-03 2.44e+04 2.66e+01 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N VAL L 28 " pdb=" CA VAL L 28 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.09e-02 8.42e+03 1.14e+01 bond pdb=" N GLU A 471 " pdb=" CA GLU A 471 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 ... (remaining 27953 not shown) Histogram of bond angle deviations from ideal: 94.33 - 102.45: 72 102.45 - 110.57: 7679 110.57 - 118.69: 14369 118.69 - 126.82: 15591 126.82 - 134.94: 313 Bond angle restraints: 38024 Sorted by residual: angle pdb=" CA TYR N 91 " pdb=" CB TYR N 91 " pdb=" CG TYR N 91 " ideal model delta sigma weight residual 113.90 127.09 -13.19 1.80e+00 3.09e-01 5.37e+01 angle pdb=" CA ARG A 905 " pdb=" CB ARG A 905 " pdb=" CG ARG A 905 " ideal model delta sigma weight residual 114.10 99.79 14.31 2.00e+00 2.50e-01 5.12e+01 angle pdb=" CB ARG A 905 " pdb=" CG ARG A 905 " pdb=" CD ARG A 905 " ideal model delta sigma weight residual 111.30 126.93 -15.63 2.30e+00 1.89e-01 4.62e+01 angle pdb=" C ASN B 282 " pdb=" CA ASN B 282 " pdb=" CB ASN B 282 " ideal model delta sigma weight residual 109.95 123.23 -13.28 1.99e+00 2.53e-01 4.45e+01 angle pdb=" C ASN A 616 " pdb=" CA ASN A 616 " pdb=" CB ASN A 616 " ideal model delta sigma weight residual 109.46 121.58 -12.12 1.84e+00 2.95e-01 4.34e+01 ... (remaining 38019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 15983 21.92 - 43.85: 913 43.85 - 65.77: 115 65.77 - 87.69: 75 87.69 - 109.61: 12 Dihedral angle restraints: 17098 sinusoidal: 7098 harmonic: 10000 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -170.42 84.42 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CA GLU B 471 " pdb=" C GLU B 471 " pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta harmonic sigma weight residual 180.00 -134.91 -45.09 0 5.00e+00 4.00e-02 8.13e+01 dihedral pdb=" CA GLN B 474 " pdb=" C GLN B 474 " pdb=" N ALA B 475 " pdb=" CA ALA B 475 " ideal model delta harmonic sigma weight residual 180.00 -136.03 -43.97 0 5.00e+00 4.00e-02 7.73e+01 ... (remaining 17095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 4392 0.306 - 0.612: 21 0.612 - 0.918: 1 0.918 - 1.223: 1 1.223 - 1.529: 1 Chirality restraints: 4416 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-01 2.50e+01 5.85e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4413 not shown) Planarity restraints: 4903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.151 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" C7 NAG D 2 " 0.043 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.200 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.124 2.00e-02 2.50e+03 1.02e-01 1.31e+02 pdb=" C7 NAG F 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.093 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.163 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.006 2.00e-02 2.50e+03 8.88e-02 9.85e+01 pdb=" CG ASN A 61 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.106 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.093 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.089 2.00e-02 2.50e+03 ... (remaining 4900 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1143 2.71 - 3.26: 27172 3.26 - 3.80: 43095 3.80 - 4.35: 53567 4.35 - 4.90: 88192 Nonbonded interactions: 213169 Sorted by model distance: nonbonded pdb=" OE2 GLU B 988 " pdb=" OG SER C 383 " model vdw 2.162 2.440 nonbonded pdb=" ND2 ASN A 394 " pdb=" OH TYR C 200 " model vdw 2.198 2.520 nonbonded pdb=" O GLU A 780 " pdb=" NE2 GLN A 784 " model vdw 2.208 2.520 nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.221 2.440 nonbonded pdb=" OG SER B 469 " pdb=" OE1 GLU B 471 " model vdw 2.230 2.440 ... (remaining 213164 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' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 501 or res \ id 503 through 524 or (resid 525 and (name N or name CA or name C or name O or n \ ame CB )) or resid 526 through 527 or (resid 528 and (name N or name CA or name \ C or name O or name CB )) or resid 529 through 1147 or resid 1301 through 1308)) \ selection = (chain 'B' and (resid 27 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O )) or resid 337 through 1147 or resid 1301 through 1308)) selection = (chain 'C' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 4.330 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: 0.030 Extract box with map and model: 19.030 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 72.850 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.200 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.007 0.088 27958 Z= 0.454 Angle : 1.390 18.637 38024 Z= 0.758 Chirality : 0.085 1.529 4416 Planarity : 0.009 0.125 4874 Dihedral : 14.420 109.615 10577 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 0.47 % Allowed : 1.11 % Favored : 98.42 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3384 helix: 0.41 (0.19), residues: 684 sheet: 0.10 (0.19), residues: 719 loop : -1.37 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP A 436 HIS 0.027 0.003 HIS C1048 PHE 0.058 0.004 PHE A 515 TYR 0.084 0.004 TYR N 91 ARG 0.024 0.002 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 455 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.7422 (m) cc_final: 0.7013 (m) REVERT: A 104 TRP cc_start: 0.6481 (m-90) cc_final: 0.6032 (m-90) REVERT: A 200 TYR cc_start: 0.8396 (m-10) cc_final: 0.7906 (m-80) REVERT: A 229 LEU cc_start: 0.9490 (mp) cc_final: 0.8962 (tt) REVERT: A 342 PHE cc_start: 0.8202 (m-10) cc_final: 0.7826 (m-80) REVERT: A 543 PHE cc_start: 0.8129 (m-80) cc_final: 0.7927 (m-10) REVERT: A 773 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7922 (tm-30) REVERT: A 777 ASN cc_start: 0.9104 (m110) cc_final: 0.8500 (m110) REVERT: A 1050 MET cc_start: 0.7913 (ptp) cc_final: 0.7705 (ptp) REVERT: B 276 LEU cc_start: 0.9362 (tp) cc_final: 0.8702 (mt) REVERT: B 546 LEU cc_start: 0.9009 (mm) cc_final: 0.7830 (tp) REVERT: B 731 MET cc_start: 0.8723 (ptm) cc_final: 0.8244 (ppp) REVERT: B 763 LEU cc_start: 0.9227 (tt) cc_final: 0.8823 (tt) REVERT: B 902 MET cc_start: 0.9328 (mmt) cc_final: 0.8953 (mmp) REVERT: B 1097 SER cc_start: 0.7951 (t) cc_final: 0.7466 (t) REVERT: B 1120 THR cc_start: 0.8367 (t) cc_final: 0.8074 (t) REVERT: C 55 PHE cc_start: 0.8573 (m-80) cc_final: 0.8113 (m-10) REVERT: C 452 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8469 (mm) REVERT: C 508 TYR cc_start: 0.8191 (m-10) cc_final: 0.7986 (m-10) REVERT: C 514 SER cc_start: 0.9209 (m) cc_final: 0.8958 (p) REVERT: C 740 MET cc_start: 0.7709 (tmm) cc_final: 0.7427 (ttt) REVERT: C 768 THR cc_start: 0.9168 (m) cc_final: 0.8912 (p) REVERT: H 1 GLN cc_start: 0.7167 (pp30) cc_final: 0.6650 (pp30) REVERT: H 6 GLN cc_start: 0.7342 (tt0) cc_final: 0.7140 (tm-30) REVERT: H 32 TYR cc_start: 0.7509 (m-10) cc_final: 0.6772 (m-10) REVERT: H 46 GLU cc_start: 0.6451 (pm20) cc_final: 0.6224 (pm20) REVERT: H 64 GLN cc_start: 0.8834 (tm-30) cc_final: 0.7888 (pt0) REVERT: H 69 ILE cc_start: 0.7460 (mm) cc_final: 0.7084 (mm) REVERT: H 80 MET cc_start: 0.7308 (tmm) cc_final: 0.6437 (ppp) REVERT: H 96 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8481 (Cg_exo) REVERT: L 5 THR cc_start: 0.8312 (m) cc_final: 0.7879 (p) REVERT: L 24 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7281 (mpp80) REVERT: L 35 TRP cc_start: 0.7143 (m100) cc_final: 0.6483 (m100) REVERT: L 54 ARG cc_start: 0.8654 (mpt90) cc_final: 0.7168 (tpp-160) REVERT: M 80 MET cc_start: 0.5682 (ppp) cc_final: 0.4702 (ppp) REVERT: M 94 ARG cc_start: 0.6777 (ptp90) cc_final: 0.6528 (ptp90) REVERT: M 100 TYR cc_start: 0.5912 (m-80) cc_final: 0.5403 (m-10) REVERT: N 4 LEU cc_start: 0.2593 (pt) cc_final: 0.2246 (pt) REVERT: N 42 GLN cc_start: 0.7836 (tp40) cc_final: 0.6814 (mt0) outliers start: 14 outliers final: 2 residues processed: 467 average time/residue: 0.3732 time to fit residues: 280.3244 Evaluate side-chains 258 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 699 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 8.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 907 ASN A 928 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 GLN B 501 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1010 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 498 GLN C 762 GLN C 955 ASN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 27958 Z= 0.371 Angle : 0.816 11.296 38024 Z= 0.426 Chirality : 0.053 0.658 4416 Planarity : 0.006 0.093 4874 Dihedral : 9.259 74.018 4520 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 2.33 % Allowed : 11.67 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3384 helix: 0.69 (0.19), residues: 693 sheet: 0.09 (0.18), residues: 734 loop : -1.48 (0.13), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 436 HIS 0.008 0.002 HIS A1048 PHE 0.022 0.002 PHE C1089 TYR 0.029 0.002 TYR C 904 ARG 0.009 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 237 time to evaluate : 3.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9519 (mp) cc_final: 0.9045 (tt) REVERT: A 460 ASN cc_start: 0.7777 (m-40) cc_final: 0.7219 (p0) REVERT: A 505 TYR cc_start: 0.8529 (m-80) cc_final: 0.8326 (m-80) REVERT: A 777 ASN cc_start: 0.9004 (m110) cc_final: 0.8541 (m110) REVERT: A 817 PHE cc_start: 0.8512 (m-80) cc_final: 0.8262 (m-80) REVERT: A 900 MET cc_start: 0.8851 (mmm) cc_final: 0.8604 (mmm) REVERT: A 970 PHE cc_start: 0.7172 (m-80) cc_final: 0.6843 (m-80) REVERT: B 697 MET cc_start: 0.8134 (tpp) cc_final: 0.6649 (tpp) REVERT: B 731 MET cc_start: 0.8970 (ptm) cc_final: 0.8320 (ppp) REVERT: B 1031 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 452 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 508 TYR cc_start: 0.8254 (m-10) cc_final: 0.7941 (m-10) REVERT: H 1 GLN cc_start: 0.6899 (pp30) cc_final: 0.6330 (pp30) REVERT: H 6 GLN cc_start: 0.6943 (tt0) cc_final: 0.6667 (tm-30) REVERT: H 32 TYR cc_start: 0.7599 (m-10) cc_final: 0.7054 (m-10) REVERT: H 48 MET cc_start: 0.5057 (mtt) cc_final: 0.4494 (mmm) REVERT: H 54 PHE cc_start: 0.9109 (t80) cc_final: 0.8770 (t80) REVERT: H 69 ILE cc_start: 0.7721 (mm) cc_final: 0.7427 (mm) REVERT: H 96 PRO cc_start: 0.9257 (Cg_endo) cc_final: 0.8742 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8707 (mpt90) cc_final: 0.7362 (tpp80) REVERT: M 48 MET cc_start: 0.3963 (mpp) cc_final: 0.3731 (mpp) REVERT: M 79 TYR cc_start: 0.9192 (m-80) cc_final: 0.8988 (m-10) REVERT: M 94 ARG cc_start: 0.6999 (ptp90) cc_final: 0.6690 (ptp90) REVERT: M 96 PRO cc_start: 0.7609 (Cg_exo) cc_final: 0.7343 (Cg_endo) REVERT: N 36 TYR cc_start: 0.7378 (m-10) cc_final: 0.6848 (m-10) REVERT: N 58 ILE cc_start: 0.5228 (OUTLIER) cc_final: 0.4910 (mt) REVERT: N 71 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.6922 (m-80) outliers start: 69 outliers final: 45 residues processed: 288 average time/residue: 0.3572 time to fit residues: 171.4773 Evaluate side-chains 230 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 295 PRO Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 311 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 308 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 ASN A 804 GLN A 928 ASN A 954 GLN ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 27958 Z= 0.330 Angle : 0.719 10.490 38024 Z= 0.379 Chirality : 0.049 0.466 4416 Planarity : 0.005 0.068 4874 Dihedral : 8.135 59.633 4520 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.00 % Allowed : 14.16 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3384 helix: 0.79 (0.19), residues: 690 sheet: -0.19 (0.18), residues: 742 loop : -1.43 (0.13), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 353 HIS 0.008 0.001 HIS A1048 PHE 0.021 0.002 PHE C1089 TYR 0.035 0.002 TYR M 100E ARG 0.008 0.001 ARG L 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 205 time to evaluate : 3.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9538 (mp) cc_final: 0.9133 (tt) REVERT: A 275 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7746 (t80) REVERT: A 460 ASN cc_start: 0.7845 (m-40) cc_final: 0.7312 (p0) REVERT: A 582 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7956 (tp) REVERT: A 731 MET cc_start: 0.8871 (ppp) cc_final: 0.7998 (ppp) REVERT: A 777 ASN cc_start: 0.9125 (m110) cc_final: 0.8790 (m110) REVERT: A 817 PHE cc_start: 0.8547 (m-80) cc_final: 0.8191 (m-80) REVERT: B 351 TYR cc_start: 0.6561 (p90) cc_final: 0.5991 (p90) REVERT: B 508 TYR cc_start: 0.7791 (m-80) cc_final: 0.7355 (m-80) REVERT: B 697 MET cc_start: 0.8171 (tpp) cc_final: 0.6905 (tpp) REVERT: B 878 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9248 (mt) REVERT: B 1031 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8296 (mt-10) REVERT: C 452 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8762 (mm) REVERT: C 481 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7252 (p0) REVERT: C 508 TYR cc_start: 0.8464 (m-10) cc_final: 0.8228 (m-10) REVERT: C 754 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.8906 (pp) REVERT: C 900 MET cc_start: 0.7373 (mpp) cc_final: 0.7117 (ptp) REVERT: H 1 GLN cc_start: 0.6538 (pp30) cc_final: 0.6077 (pp30) REVERT: H 6 GLN cc_start: 0.7109 (tt0) cc_final: 0.6888 (tm-30) REVERT: H 54 PHE cc_start: 0.9104 (t80) cc_final: 0.8574 (t80) REVERT: H 96 PRO cc_start: 0.9118 (Cg_endo) cc_final: 0.8870 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8809 (mpt90) cc_final: 0.7332 (tpp80) REVERT: M 101 ASP cc_start: 0.7770 (p0) cc_final: 0.7423 (p0) REVERT: N 36 TYR cc_start: 0.7914 (m-10) cc_final: 0.7708 (m-80) REVERT: N 42 GLN cc_start: 0.7877 (tp40) cc_final: 0.6826 (mt0) REVERT: N 71 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6443 (m-80) outliers start: 89 outliers final: 53 residues processed: 272 average time/residue: 0.3469 time to fit residues: 158.2056 Evaluate side-chains 240 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 180 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 312 optimal weight: 0.6980 chunk 330 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 295 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27958 Z= 0.185 Angle : 0.630 10.675 38024 Z= 0.322 Chirality : 0.047 0.456 4416 Planarity : 0.004 0.056 4874 Dihedral : 7.411 59.743 4520 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.00 % Allowed : 15.85 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3384 helix: 1.03 (0.19), residues: 679 sheet: -0.19 (0.18), residues: 750 loop : -1.33 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.007 0.001 HIS A1048 PHE 0.017 0.001 PHE C 429 TYR 0.019 0.001 TYR L 91 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 219 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9538 (mp) cc_final: 0.9106 (tt) REVERT: A 460 ASN cc_start: 0.7811 (m-40) cc_final: 0.7258 (p0) REVERT: A 582 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8033 (tp) REVERT: A 720 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8744 (mt) REVERT: A 731 MET cc_start: 0.8799 (ppp) cc_final: 0.7931 (ppp) REVERT: A 777 ASN cc_start: 0.9020 (m110) cc_final: 0.8679 (m110) REVERT: A 817 PHE cc_start: 0.8514 (m-80) cc_final: 0.8145 (m-80) REVERT: B 284 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8929 (t) REVERT: B 508 TYR cc_start: 0.7804 (m-80) cc_final: 0.7392 (m-80) REVERT: B 697 MET cc_start: 0.7984 (tpp) cc_final: 0.6933 (tpp) REVERT: B 731 MET cc_start: 0.9128 (ptm) cc_final: 0.8611 (ppp) REVERT: B 774 GLN cc_start: 0.8948 (mt0) cc_final: 0.8670 (mm-40) REVERT: B 821 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 878 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9261 (mt) REVERT: B 1012 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9437 (mm) REVERT: B 1031 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 1067 TYR cc_start: 0.8159 (t80) cc_final: 0.7821 (t80) REVERT: C 508 TYR cc_start: 0.8517 (m-10) cc_final: 0.8259 (m-10) REVERT: C 697 MET cc_start: 0.9018 (tmm) cc_final: 0.8645 (tmm) REVERT: C 754 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.8893 (pp) REVERT: C 900 MET cc_start: 0.7246 (mpp) cc_final: 0.6983 (ptp) REVERT: H 1 GLN cc_start: 0.6454 (pp30) cc_final: 0.5925 (pp30) REVERT: H 6 GLN cc_start: 0.6923 (tt0) cc_final: 0.6688 (tm-30) REVERT: H 32 TYR cc_start: 0.7560 (m-10) cc_final: 0.7231 (m-10) REVERT: H 54 PHE cc_start: 0.9139 (t80) cc_final: 0.8561 (t80) REVERT: H 96 PRO cc_start: 0.8958 (Cg_endo) cc_final: 0.8673 (Cg_exo) REVERT: H 98 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: L 46 LEU cc_start: 0.7641 (tp) cc_final: 0.7319 (mt) REVERT: L 54 ARG cc_start: 0.8762 (mpt90) cc_final: 0.7290 (ttm-80) REVERT: M 48 MET cc_start: 0.3679 (mpp) cc_final: 0.2415 (mpp) REVERT: N 36 TYR cc_start: 0.7922 (m-10) cc_final: 0.7483 (m-80) REVERT: N 42 GLN cc_start: 0.8027 (tp40) cc_final: 0.7028 (mt0) REVERT: N 70 ASP cc_start: 0.9094 (m-30) cc_final: 0.8235 (t0) REVERT: N 71 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7140 (m-80) outliers start: 89 outliers final: 50 residues processed: 283 average time/residue: 0.3406 time to fit residues: 162.3470 Evaluate side-chains 255 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 196 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 30.0000 chunk 282 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 296 optimal weight: 0.7980 chunk 83 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 784 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 27958 Z= 0.329 Angle : 0.690 9.721 38024 Z= 0.359 Chirality : 0.047 0.399 4416 Planarity : 0.005 0.060 4874 Dihedral : 7.211 58.881 4518 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.98 % Allowed : 17.19 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3384 helix: 0.83 (0.19), residues: 682 sheet: -0.41 (0.18), residues: 772 loop : -1.27 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 103 HIS 0.007 0.002 HIS A1048 PHE 0.031 0.002 PHE M 54 TYR 0.019 0.002 TYR C 904 ARG 0.007 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 194 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9582 (mp) cc_final: 0.9135 (tt) REVERT: A 582 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8150 (tp) REVERT: A 720 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8690 (mt) REVERT: A 731 MET cc_start: 0.8895 (ppp) cc_final: 0.8074 (ppp) REVERT: A 777 ASN cc_start: 0.9147 (m110) cc_final: 0.8834 (m110) REVERT: A 817 PHE cc_start: 0.8532 (m-80) cc_final: 0.8157 (m-80) REVERT: B 821 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9093 (tt) REVERT: B 1031 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8282 (mt-10) REVERT: C 369 TYR cc_start: 0.8741 (t80) cc_final: 0.8297 (t80) REVERT: C 508 TYR cc_start: 0.8583 (m-10) cc_final: 0.8329 (m-10) REVERT: C 873 TYR cc_start: 0.9193 (OUTLIER) cc_final: 0.8926 (m-10) REVERT: C 900 MET cc_start: 0.7639 (mpp) cc_final: 0.7389 (ptp) REVERT: H 1 GLN cc_start: 0.6451 (pp30) cc_final: 0.5981 (pp30) REVERT: H 54 PHE cc_start: 0.9147 (t80) cc_final: 0.8576 (t80) REVERT: H 67 LEU cc_start: 0.8347 (mt) cc_final: 0.7607 (pp) REVERT: H 96 PRO cc_start: 0.8872 (Cg_endo) cc_final: 0.8510 (Cg_exo) REVERT: L 24 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6878 (mpp-170) REVERT: L 54 ARG cc_start: 0.8799 (mpt90) cc_final: 0.7450 (tpp-160) REVERT: L 77 ARG cc_start: 0.8312 (ttp80) cc_final: 0.7914 (ttp80) REVERT: M 48 MET cc_start: 0.3553 (mpp) cc_final: 0.2847 (mpp) REVERT: N 36 TYR cc_start: 0.7895 (m-10) cc_final: 0.7489 (m-80) REVERT: N 71 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6426 (m-80) outliers start: 118 outliers final: 75 residues processed: 289 average time/residue: 0.3480 time to fit residues: 168.3576 Evaluate side-chains 251 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 171 time to evaluate : 3.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 820 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 20.0000 chunk 297 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 330 optimal weight: 8.9990 chunk 274 optimal weight: 0.9980 chunk 153 optimal weight: 5.9990 chunk 27 optimal weight: 0.0270 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27958 Z= 0.163 Angle : 0.627 11.279 38024 Z= 0.314 Chirality : 0.047 0.415 4416 Planarity : 0.004 0.049 4874 Dihedral : 6.706 58.729 4518 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.83 % Allowed : 19.25 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3384 helix: 1.15 (0.20), residues: 680 sheet: -0.36 (0.18), residues: 765 loop : -1.20 (0.14), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.007 0.001 HIS A1048 PHE 0.019 0.001 PHE C 429 TYR 0.019 0.001 TYR B 495 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 198 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9559 (mp) cc_final: 0.9114 (tt) REVERT: A 582 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8076 (tp) REVERT: A 731 MET cc_start: 0.8812 (ppp) cc_final: 0.7936 (ppp) REVERT: A 777 ASN cc_start: 0.8998 (m110) cc_final: 0.8719 (m-40) REVERT: A 817 PHE cc_start: 0.8490 (m-80) cc_final: 0.8128 (m-80) REVERT: A 934 ILE cc_start: 0.9260 (mm) cc_final: 0.9009 (mm) REVERT: A 1082 CYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4917 (t) REVERT: B 408 ARG cc_start: 0.6551 (mtp180) cc_final: 0.6031 (mtp180) REVERT: B 697 MET cc_start: 0.8021 (tpp) cc_final: 0.7685 (tpt) REVERT: B 731 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8392 (ptm) REVERT: B 821 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9055 (tt) REVERT: B 867 ASP cc_start: 0.8978 (p0) cc_final: 0.8586 (p0) REVERT: B 896 ILE cc_start: 0.9227 (pt) cc_final: 0.8958 (mm) REVERT: B 1031 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8185 (mt-10) REVERT: C 55 PHE cc_start: 0.8746 (m-80) cc_final: 0.8227 (m-80) REVERT: C 508 TYR cc_start: 0.8575 (m-10) cc_final: 0.8321 (m-10) REVERT: C 697 MET cc_start: 0.9028 (tmm) cc_final: 0.8614 (tmm) REVERT: C 878 LEU cc_start: 0.9464 (mt) cc_final: 0.9245 (tp) REVERT: C 900 MET cc_start: 0.7512 (mpp) cc_final: 0.7179 (ptp) REVERT: H 1 GLN cc_start: 0.6402 (pp30) cc_final: 0.5920 (pp30) REVERT: H 48 MET cc_start: 0.4943 (mtt) cc_final: 0.4538 (mmm) REVERT: H 54 PHE cc_start: 0.9155 (t80) cc_final: 0.8572 (t80) REVERT: H 67 LEU cc_start: 0.8122 (mt) cc_final: 0.7554 (pp) REVERT: H 96 PRO cc_start: 0.8870 (Cg_endo) cc_final: 0.8550 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8786 (mpt90) cc_final: 0.7466 (tpp80) REVERT: L 77 ARG cc_start: 0.8296 (ttp80) cc_final: 0.8072 (ptm-80) REVERT: M 48 MET cc_start: 0.3485 (mpp) cc_final: 0.2712 (mpp) REVERT: M 91 TYR cc_start: 0.6967 (m-80) cc_final: 0.6718 (m-80) REVERT: N 13 LEU cc_start: 0.4916 (mt) cc_final: 0.4702 (mm) REVERT: N 36 TYR cc_start: 0.7828 (m-10) cc_final: 0.7426 (m-80) REVERT: N 70 ASP cc_start: 0.9149 (m-30) cc_final: 0.8299 (t0) REVERT: N 71 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7160 (m-80) outliers start: 84 outliers final: 56 residues processed: 259 average time/residue: 0.3549 time to fit residues: 154.3613 Evaluate side-chains 243 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 182 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 777 ASN Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 71 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 chunk 241 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 278 optimal weight: 0.5980 chunk 184 optimal weight: 1.9990 chunk 329 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN L 27 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27958 Z= 0.166 Angle : 0.612 12.183 38024 Z= 0.307 Chirality : 0.046 0.396 4416 Planarity : 0.004 0.047 4874 Dihedral : 6.378 59.699 4518 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.17 % Allowed : 19.29 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3384 helix: 1.22 (0.20), residues: 683 sheet: -0.41 (0.18), residues: 782 loop : -1.17 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS A1048 PHE 0.018 0.001 PHE C 429 TYR 0.018 0.001 TYR H 98 ARG 0.006 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 204 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9551 (mp) cc_final: 0.9102 (tt) REVERT: A 582 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (tp) REVERT: A 731 MET cc_start: 0.8778 (ppp) cc_final: 0.7936 (ppp) REVERT: A 773 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 777 ASN cc_start: 0.8937 (m110) cc_final: 0.8494 (m-40) REVERT: A 817 PHE cc_start: 0.8503 (m-80) cc_final: 0.8144 (m-80) REVERT: A 896 ILE cc_start: 0.8114 (tp) cc_final: 0.7821 (pt) REVERT: A 1082 CYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4907 (t) REVERT: B 298 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: B 697 MET cc_start: 0.8104 (tpp) cc_final: 0.7276 (tpp) REVERT: B 731 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8388 (ptm) REVERT: B 821 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9092 (tt) REVERT: B 896 ILE cc_start: 0.9217 (pt) cc_final: 0.8958 (mm) REVERT: B 1031 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8163 (mt-10) REVERT: C 55 PHE cc_start: 0.8653 (m-80) cc_final: 0.8101 (m-80) REVERT: C 508 TYR cc_start: 0.8565 (m-10) cc_final: 0.8290 (m-10) REVERT: C 878 LEU cc_start: 0.9468 (mt) cc_final: 0.9256 (tp) REVERT: C 1050 MET cc_start: 0.8415 (ppp) cc_final: 0.8092 (ppp) REVERT: H 1 GLN cc_start: 0.6492 (pp30) cc_final: 0.6012 (pp30) REVERT: H 46 GLU cc_start: 0.6980 (pm20) cc_final: 0.6652 (pm20) REVERT: H 54 PHE cc_start: 0.9122 (t80) cc_final: 0.8484 (t80) REVERT: H 67 LEU cc_start: 0.8110 (mt) cc_final: 0.7330 (pp) REVERT: H 96 PRO cc_start: 0.8843 (Cg_endo) cc_final: 0.8584 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8812 (mpt90) cc_final: 0.7403 (tpp80) REVERT: M 91 TYR cc_start: 0.7040 (m-80) cc_final: 0.6811 (m-80) REVERT: N 70 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8353 (t0) outliers start: 94 outliers final: 62 residues processed: 274 average time/residue: 0.3528 time to fit residues: 161.6004 Evaluate side-chains 254 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 186 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 9.9990 chunk 131 optimal weight: 50.0000 chunk 196 optimal weight: 1.9990 chunk 99 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 224 optimal weight: 9.9990 chunk 162 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 259 optimal weight: 0.4980 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27958 Z= 0.176 Angle : 0.609 12.093 38024 Z= 0.307 Chirality : 0.046 0.388 4416 Planarity : 0.004 0.046 4874 Dihedral : 6.117 59.061 4517 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.03 % Allowed : 20.09 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3384 helix: 1.23 (0.20), residues: 686 sheet: -0.41 (0.18), residues: 754 loop : -1.15 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 PHE 0.041 0.001 PHE M 54 TYR 0.019 0.001 TYR M 79 ARG 0.007 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 192 time to evaluate : 3.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9563 (mp) cc_final: 0.9110 (tt) REVERT: A 582 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8092 (tp) REVERT: A 731 MET cc_start: 0.8765 (ppp) cc_final: 0.7932 (ppp) REVERT: A 773 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7994 (tm-30) REVERT: A 777 ASN cc_start: 0.8895 (m110) cc_final: 0.8438 (m-40) REVERT: A 817 PHE cc_start: 0.8505 (m-80) cc_final: 0.8137 (m-80) REVERT: A 896 ILE cc_start: 0.8091 (tp) cc_final: 0.7791 (pt) REVERT: A 1082 CYS cc_start: 0.5226 (OUTLIER) cc_final: 0.4948 (t) REVERT: B 697 MET cc_start: 0.8118 (tpp) cc_final: 0.7335 (tpp) REVERT: B 731 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8445 (ptm) REVERT: B 773 GLU cc_start: 0.9050 (tt0) cc_final: 0.8500 (pt0) REVERT: B 821 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9130 (tt) REVERT: B 896 ILE cc_start: 0.9234 (pt) cc_final: 0.8995 (mm) REVERT: B 1031 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8128 (mt-10) REVERT: C 55 PHE cc_start: 0.8653 (m-80) cc_final: 0.8127 (m-80) REVERT: C 495 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7333 (t80) REVERT: C 508 TYR cc_start: 0.8552 (m-10) cc_final: 0.8269 (m-10) REVERT: C 697 MET cc_start: 0.9038 (tmm) cc_final: 0.8762 (tmm) REVERT: C 878 LEU cc_start: 0.9473 (mt) cc_final: 0.9262 (tp) REVERT: C 1050 MET cc_start: 0.8289 (ppp) cc_final: 0.8045 (ppp) REVERT: H 1 GLN cc_start: 0.6471 (pp30) cc_final: 0.6010 (pp30) REVERT: H 46 GLU cc_start: 0.7022 (pm20) cc_final: 0.6664 (pm20) REVERT: H 54 PHE cc_start: 0.9134 (t80) cc_final: 0.8494 (t80) REVERT: H 67 LEU cc_start: 0.8138 (mt) cc_final: 0.7471 (tp) REVERT: H 96 PRO cc_start: 0.8818 (Cg_endo) cc_final: 0.8500 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8772 (mpt90) cc_final: 0.7364 (tpp80) REVERT: M 48 MET cc_start: 0.3591 (mpp) cc_final: 0.2526 (mpp) REVERT: M 91 TYR cc_start: 0.7016 (m-80) cc_final: 0.6680 (m-80) REVERT: N 70 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8375 (t0) outliers start: 90 outliers final: 67 residues processed: 260 average time/residue: 0.3521 time to fit residues: 153.1309 Evaluate side-chains 255 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 182 time to evaluate : 3.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.0570 chunk 315 optimal weight: 0.5980 chunk 288 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 133 optimal weight: 30.0000 chunk 241 optimal weight: 10.0000 chunk 94 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27958 Z= 0.172 Angle : 0.612 13.063 38024 Z= 0.304 Chirality : 0.046 0.380 4416 Planarity : 0.004 0.047 4874 Dihedral : 5.934 58.707 4517 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer: Outliers : 2.60 % Allowed : 20.60 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.14), residues: 3384 helix: 1.29 (0.20), residues: 684 sheet: -0.39 (0.18), residues: 781 loop : -1.14 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.007 0.001 HIS A1048 PHE 0.032 0.001 PHE M 54 TYR 0.015 0.001 TYR H 98 ARG 0.005 0.000 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 200 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9570 (mp) cc_final: 0.9106 (tt) REVERT: A 402 ILE cc_start: 0.7535 (pt) cc_final: 0.7331 (pt) REVERT: A 582 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8115 (tp) REVERT: A 731 MET cc_start: 0.8731 (ppp) cc_final: 0.7914 (ppp) REVERT: A 773 GLU cc_start: 0.8277 (tm-30) cc_final: 0.8012 (tm-30) REVERT: A 777 ASN cc_start: 0.8820 (m110) cc_final: 0.8400 (m-40) REVERT: A 817 PHE cc_start: 0.8500 (m-80) cc_final: 0.8137 (m-80) REVERT: A 896 ILE cc_start: 0.8097 (tp) cc_final: 0.7803 (pt) REVERT: A 1050 MET cc_start: 0.7797 (ptp) cc_final: 0.7563 (ptp) REVERT: A 1082 CYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4887 (t) REVERT: B 298 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: B 697 MET cc_start: 0.8150 (tpp) cc_final: 0.7416 (tpp) REVERT: B 731 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8405 (ptm) REVERT: B 773 GLU cc_start: 0.8997 (tt0) cc_final: 0.8523 (pt0) REVERT: B 821 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9170 (tt) REVERT: B 869 MET cc_start: 0.9327 (ptp) cc_final: 0.9036 (ptp) REVERT: B 896 ILE cc_start: 0.9233 (pt) cc_final: 0.8952 (mm) REVERT: B 1031 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 55 PHE cc_start: 0.8672 (m-80) cc_final: 0.8036 (m-10) REVERT: C 495 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7357 (t80) REVERT: C 508 TYR cc_start: 0.8569 (m-10) cc_final: 0.8280 (m-10) REVERT: C 697 MET cc_start: 0.9079 (tmm) cc_final: 0.8697 (tmm) REVERT: C 740 MET cc_start: 0.8310 (ttt) cc_final: 0.7907 (tmm) REVERT: H 1 GLN cc_start: 0.6460 (pp30) cc_final: 0.5987 (pp30) REVERT: H 46 GLU cc_start: 0.7096 (pm20) cc_final: 0.6647 (pm20) REVERT: H 54 PHE cc_start: 0.9165 (t80) cc_final: 0.8489 (t80) REVERT: H 67 LEU cc_start: 0.8191 (mt) cc_final: 0.7351 (tp) REVERT: H 96 PRO cc_start: 0.8815 (Cg_endo) cc_final: 0.8500 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8767 (mpt90) cc_final: 0.7357 (tpp80) REVERT: M 91 TYR cc_start: 0.7038 (m-80) cc_final: 0.6696 (m-80) REVERT: N 70 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8377 (t0) outliers start: 77 outliers final: 64 residues processed: 259 average time/residue: 0.3637 time to fit residues: 157.4502 Evaluate side-chains 254 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 183 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 340 optimal weight: 7.9990 chunk 313 optimal weight: 8.9990 chunk 271 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 209 optimal weight: 20.0000 chunk 166 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27958 Z= 0.187 Angle : 0.609 12.435 38024 Z= 0.305 Chirality : 0.046 0.369 4416 Planarity : 0.004 0.052 4874 Dihedral : 5.833 58.035 4517 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 2.46 % Allowed : 20.84 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3384 helix: 1.33 (0.20), residues: 681 sheet: -0.38 (0.18), residues: 782 loop : -1.12 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 PHE 0.029 0.001 PHE M 54 TYR 0.017 0.001 TYR B 396 ARG 0.004 0.000 ARG A1014 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 191 time to evaluate : 4.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.9564 (mp) cc_final: 0.9120 (tt) REVERT: A 582 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8154 (tp) REVERT: A 731 MET cc_start: 0.8723 (ppp) cc_final: 0.7932 (ppp) REVERT: A 770 ILE cc_start: 0.9555 (OUTLIER) cc_final: 0.9085 (mt) REVERT: A 817 PHE cc_start: 0.8496 (m-80) cc_final: 0.8128 (m-80) REVERT: A 896 ILE cc_start: 0.8221 (tp) cc_final: 0.7935 (pt) REVERT: A 1082 CYS cc_start: 0.5319 (OUTLIER) cc_final: 0.5041 (t) REVERT: B 697 MET cc_start: 0.8180 (tpp) cc_final: 0.7454 (tpp) REVERT: B 731 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8292 (ptm) REVERT: B 773 GLU cc_start: 0.8976 (tt0) cc_final: 0.8487 (pt0) REVERT: B 821 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9201 (tt) REVERT: B 896 ILE cc_start: 0.9241 (pt) cc_final: 0.8957 (mm) REVERT: B 1031 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 1050 MET cc_start: 0.7935 (ptm) cc_final: 0.7341 (ptp) REVERT: C 55 PHE cc_start: 0.8663 (m-80) cc_final: 0.8131 (m-80) REVERT: C 452 LEU cc_start: 0.9146 (mm) cc_final: 0.8835 (mm) REVERT: C 495 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.7298 (t80) REVERT: C 508 TYR cc_start: 0.8552 (m-10) cc_final: 0.8253 (m-10) REVERT: C 740 MET cc_start: 0.8338 (ttt) cc_final: 0.7919 (tmm) REVERT: H 1 GLN cc_start: 0.6448 (pp30) cc_final: 0.5980 (pp30) REVERT: H 54 PHE cc_start: 0.9142 (t80) cc_final: 0.8473 (t80) REVERT: H 67 LEU cc_start: 0.8115 (mt) cc_final: 0.7487 (tp) REVERT: H 96 PRO cc_start: 0.8786 (Cg_endo) cc_final: 0.8462 (Cg_exo) REVERT: L 54 ARG cc_start: 0.8763 (mpt90) cc_final: 0.7283 (ttm-80) REVERT: M 48 MET cc_start: 0.3469 (mpp) cc_final: 0.2425 (mpp) REVERT: N 70 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8380 (t0) outliers start: 73 outliers final: 63 residues processed: 246 average time/residue: 0.3513 time to fit residues: 145.3636 Evaluate side-chains 257 residues out of total 2987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 187 time to evaluate : 3.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 462 LYS Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 10 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 70 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 40 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 271 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS A1119 ASN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.074483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053280 restraints weight = 140736.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.054837 restraints weight = 75760.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055869 restraints weight = 48922.910| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 27958 Z= 0.156 Angle : 0.603 12.874 38024 Z= 0.301 Chirality : 0.046 0.371 4416 Planarity : 0.004 0.055 4874 Dihedral : 5.694 58.273 4517 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.96 % Favored : 95.01 % Rotamer: Outliers : 2.63 % Allowed : 20.84 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 3384 helix: 1.38 (0.20), residues: 677 sheet: -0.36 (0.18), residues: 786 loop : -1.10 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.006 0.001 HIS A1048 PHE 0.026 0.001 PHE M 54 TYR 0.017 0.001 TYR L 87 ARG 0.004 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5016.52 seconds wall clock time: 94 minutes 9.86 seconds (5649.86 seconds total)