Starting phenix.real_space_refine on Fri Apr 12 14:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p9y_17578/04_2024/8p9y_17578_neut_updated.pdb" } resolution = 4.3 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 117 5.16 5 Na 3 4.78 5 C 16518 2.51 5 N 4256 2.21 5 O 5043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ARG 1107": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25937 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8425 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 54, 'TRANS': 1025} Chain breaks: 4 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 8426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1081, 8426 Classifications: {'peptide': 1081} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 54, 'TRANS': 1026} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8374 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 54, 'TRANS': 1021} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 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: 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: "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: 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: "H" 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: "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: "J" 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: "K" 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: "L" 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: "M" 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 128 Unusual residues: {' NA': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 178 Unusual residues: {' NA': 1, 'NAG': 6, 'XIO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="NA NA A1310 " occ=0.00 residue: pdb="NA NA A1311 " occ=0.00 residue: pdb=" C02 XIO C1307 " occ=0.00 ... (91 atoms not shown) pdb=" S76 XIO C1307 " occ=0.00 residue: pdb="NA NA C1308 " occ=0.00 Time building chain proxies: 13.60, per 1000 atoms: 0.52 Number of scatterers: 25937 At special positions: 0 Unit cell: (149.625, 161.595, 174.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 117 16.00 Na 3 11.00 O 5043 8.00 N 4256 7.00 C 16518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.78 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.97 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.08 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.05 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=1.95 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.97 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.07 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.01 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.00 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.91 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.82 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.79 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.82 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.01 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.88 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.93 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=1.99 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.97 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.06 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.01 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.05 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 "HETATM25659 O5 NAG B1302 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A1301 " - " ASN A 234 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 801 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A1098 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 164 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG C1301 " - " ASN C1134 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 801 " " NAG C1306 " - " ASN C 616 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 164 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 331 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 343 " " NAG K 1 " - " ASN C 717 " " NAG L 1 " - " ASN C 282 " " NAG M 1 " - " ASN C 343 " Time building additional restraints: 10.43 Conformation dependent library (CDL) restraints added in 5.0 seconds 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6056 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 44 sheets defined 21.0% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 634 through 637 No H-bonds generated for 'chain 'A' and resid 634 through 637' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.589A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 812 through 814 No H-bonds generated for 'chain 'A' and resid 812 through 814' Processing helix chain 'A' and resid 817 through 828 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.505A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.039A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1030 Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.919A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 366 through 369 No H-bonds generated for 'chain 'B' and resid 366 through 369' Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.942A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.590A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 817 through 829 removed outlier: 3.596A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 887 through 890 No H-bonds generated for 'chain 'B' and resid 887 through 890' Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 940 Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.503A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1031 removed outlier: 5.860A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 997 " --> pdb=" O ILE B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 350 through 352 No H-bonds generated for 'chain 'C' and resid 350 through 352' Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 404 through 407 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.673A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.615A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 814 No H-bonds generated for 'chain 'C' and resid 812 through 814' Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 898 through 909 removed outlier: 3.749A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.927A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 944 through 966 removed outlier: 4.148A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 959 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 966 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1031 removed outlier: 4.222A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.996A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.634A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.504A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 117 through 121 removed outlier: 4.496A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 243 through 246 removed outlier: 7.019A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 195 through 197 Processing sheet with id= F, first strand: chain 'A' and resid 324 through 327 removed outlier: 4.179A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.707A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 648 through 651 removed outlier: 3.602A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 693 through 695 removed outlier: 3.529A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.649A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= L, first strand: chain 'A' and resid 1080 through 1082 removed outlier: 3.595A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1088 through 1090 removed outlier: 3.587A pdb=" N PHE A1121 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id= O, first strand: chain 'A' and resid 711 through 717 removed outlier: 6.565A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.052A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 48 through 52 removed outlier: 4.153A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 104 through 107 Processing sheet with id= S, first strand: chain 'B' and resid 117 through 121 removed outlier: 3.504A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 243 through 246 removed outlier: 7.090A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'B' and resid 324 through 328 Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.193A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= X, first strand: chain 'B' and resid 472 through 474 Processing sheet with id= Y, first strand: chain 'B' and resid 551 through 554 removed outlier: 3.702A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 649 through 651 removed outlier: 4.027A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 691 through 696 removed outlier: 3.538A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.805A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 718 through 727 removed outlier: 3.929A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR B 723 " --> pdb=" O HIS B1064 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS B1064 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.147A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.773A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 104 through 107 removed outlier: 3.643A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 117 through 121 removed outlier: 3.686A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.938A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'C' and resid 195 through 197 Processing sheet with id= AK, first strand: chain 'C' and resid 311 through 314 Processing sheet with id= AL, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.495A pdb=" N ASN C 540 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ARG C 328 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN C 542 " --> pdb=" O ARG C 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.272A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 670 through 675 removed outlier: 3.693A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 718 through 727 removed outlier: 6.528A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 734 through 736 Processing sheet with id= AR, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 4.453A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C1071 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN C 717 " --> pdb=" O GLN C1071 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS C1073 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE C1075 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA C 713 " --> pdb=" O PHE C1075 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR C1077 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER C 711 " --> pdb=" O THR C1077 " (cutoff:3.500A) 749 hydrogen bonds defined for protein. 2085 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: 11.55 Time building geometry restraints manager: 11.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.08: 3 1.08 - 1.29: 4207 1.29 - 1.49: 11614 1.49 - 1.70: 10562 1.70 - 1.90: 150 Bond restraints: 26536 Sorted by residual: bond pdb=" C SER B 940 " pdb=" O SER B 940 " ideal model delta sigma weight residual 1.237 0.880 0.356 1.19e-02 7.06e+03 8.97e+02 bond pdb=" C SER A 940 " pdb=" O SER A 940 " ideal model delta sigma weight residual 1.236 0.943 0.293 1.31e-02 5.83e+03 5.00e+02 bond pdb=" C CYS B 617 " pdb=" O CYS B 617 " ideal model delta sigma weight residual 1.236 1.089 0.147 1.25e-02 6.40e+03 1.38e+02 bond pdb=" C CYS A 617 " pdb=" O CYS A 617 " ideal model delta sigma weight residual 1.236 1.376 -0.140 1.25e-02 6.40e+03 1.25e+02 bond pdb=" C THR C 676 " pdb=" O THR C 676 " ideal model delta sigma weight residual 1.231 1.007 0.224 2.00e-02 2.50e+03 1.25e+02 ... (remaining 26531 not shown) Histogram of bond angle deviations from ideal: 96.02 - 104.88: 512 104.88 - 113.75: 14473 113.75 - 122.62: 16935 122.62 - 131.48: 4163 131.48 - 140.35: 56 Bond angle restraints: 36139 Sorted by residual: angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CA PRO C 527 " ideal model delta sigma weight residual 119.56 140.35 -20.79 1.02e+00 9.61e-01 4.16e+02 angle pdb=" N86 XIO C1307 " pdb=" C75 XIO C1307 " pdb=" S76 XIO C1307 " ideal model delta sigma weight residual 66.74 125.84 -59.10 3.00e+00 1.11e-01 3.88e+02 angle pdb=" C74 XIO C1307 " pdb=" C75 XIO C1307 " pdb=" S76 XIO C1307 " ideal model delta sigma weight residual 171.95 125.86 46.09 3.00e+00 1.11e-01 2.36e+02 angle pdb=" O PHE B 515 " pdb=" C PHE B 515 " pdb=" N GLU B 516 " ideal model delta sigma weight residual 122.59 104.84 17.75 1.33e+00 5.65e-01 1.78e+02 angle pdb=" N59 XIO C1307 " pdb=" C48 XIO C1307 " pdb=" S49 XIO C1307 " ideal model delta sigma weight residual 86.48 126.04 -39.56 3.00e+00 1.11e-01 1.74e+02 ... (remaining 36134 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.14: 15313 24.14 - 48.27: 861 48.27 - 72.41: 120 72.41 - 96.55: 27 96.55 - 120.68: 3 Dihedral angle restraints: 16324 sinusoidal: 6903 harmonic: 9421 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -1.13 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " pdb=" SG CYS C 432 " pdb=" CB CYS C 432 " ideal model delta sinusoidal sigma weight residual 93.00 13.00 80.00 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C VAL C 826 " pdb=" N VAL C 826 " pdb=" CA VAL C 826 " pdb=" CB VAL C 826 " ideal model delta harmonic sigma weight residual -122.00 -142.56 20.56 0 2.50e+00 1.60e-01 6.77e+01 ... (remaining 16321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.633: 4201 0.633 - 1.266: 3 1.266 - 1.899: 0 1.899 - 2.532: 2 2.532 - 3.165: 2 Chirality restraints: 4208 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 164 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 0.77 -3.17 2.00e-01 2.50e+01 2.50e+02 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 0.50 -2.90 2.00e-01 2.50e+01 2.10e+02 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.40 -2.00 2.00e-01 2.50e+01 1.00e+02 ... (remaining 4205 not shown) Planarity restraints: 4661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C73 XIO C1307 " -0.031 2.00e-02 2.50e+03 1.39e-01 5.35e+02 pdb=" C74 XIO C1307 " -0.072 2.00e-02 2.50e+03 pdb=" C75 XIO C1307 " -0.040 2.00e-02 2.50e+03 pdb=" C87 XIO C1307 " -0.183 2.00e-02 2.50e+03 pdb=" C88 XIO C1307 " -0.162 2.00e-02 2.50e+03 pdb=" C89 XIO C1307 " 0.013 2.00e-02 2.50e+03 pdb=" C90 XIO C1307 " 0.168 2.00e-02 2.50e+03 pdb=" C91 XIO C1307 " 0.149 2.00e-02 2.50e+03 pdb=" C92 XIO C1307 " -0.024 2.00e-02 2.50e+03 pdb=" N86 XIO C1307 " -0.108 2.00e-02 2.50e+03 pdb=" S76 XIO C1307 " 0.289 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C02 XIO C1307 " -0.046 2.00e-02 2.50e+03 1.69e-01 3.57e+02 pdb=" C03 XIO C1307 " 0.145 2.00e-02 2.50e+03 pdb=" C72 XIO C1307 " 0.211 2.00e-02 2.50e+03 pdb=" N71 XIO C1307 " -0.270 2.00e-02 2.50e+03 pdb=" O01 XIO C1307 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C42 XIO C1307 " 0.131 2.00e-02 2.50e+03 1.56e-01 3.05e+02 pdb=" C43 XIO C1307 " -0.029 2.00e-02 2.50e+03 pdb=" C45 XIO C1307 " 0.195 2.00e-02 2.50e+03 pdb=" N44 XIO C1307 " -0.253 2.00e-02 2.50e+03 pdb=" O70 XIO C1307 " -0.044 2.00e-02 2.50e+03 ... (remaining 4658 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 24 1.87 - 2.63: 751 2.63 - 3.38: 36158 3.38 - 4.14: 61462 4.14 - 4.90: 105101 Nonbonded interactions: 203496 Sorted by model distance: nonbonded pdb=" CG ARG B 328 " pdb=" CB ASP B 578 " model vdw 1.112 3.840 nonbonded pdb=" NH2 ARG C 328 " pdb=" OG1 THR C 581 " model vdw 1.374 2.520 nonbonded pdb=" CZ3 TRP C 353 " pdb=" CD1 TYR C 423 " model vdw 1.521 3.640 nonbonded pdb=" NE ARG C 328 " pdb=" OD2 ASP C 578 " model vdw 1.549 2.520 nonbonded pdb=" NH1 ARG B 328 " pdb=" CG2 THR B 581 " model vdw 1.609 3.540 ... (remaining 203491 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 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 579 or (resid 580 and (name N o \ r name CA or name C or name O or name CB )) or resid 581 through 616 or (resid 6 \ 17 and (name N or name CA or name C or name CB or name SG )) or resid 618 throug \ h 621 or resid 641 through 939 or (resid 940 through 944 and (name N or name CA \ or name C or name O or name CB )) or resid 945 through 1146 or resid 1301 throug \ h 1306)) selection = (chain 'B' and (resid 15 through 402 or (resid 403 and (name N or name CA or nam \ e C or name O or name CB )) or resid 404 through 616 or (resid 617 and (name N o \ r name CA or name C or name CB or name SG )) or resid 618 through 621 or resid 6 \ 41 through 829 or resid 854 through 939 or (resid 940 through 944 and (name N or \ name CA or name C or name O or name CB )) or resid 945 through 1146 or resid 13 \ 01 through 1306)) selection = (chain 'C' and (resid 15 through 579 or (resid 580 and (name N or name CA or nam \ e C or name O or name CB )) or resid 581 through 829 or resid 854 through 1146 o \ r resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } 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=0.00 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: 8.910 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: 24.680 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 71.520 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.250 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 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 : 0.012 0.356 26536 Z= 0.775 Angle : 1.600 59.098 36139 Z= 0.969 Chirality : 0.122 3.165 4208 Planarity : 0.009 0.169 4627 Dihedral : 14.361 120.683 10145 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 59.14 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.99 % Favored : 95.48 % Rotamer: Outliers : 7.52 % Allowed : 10.77 % Favored : 81.70 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3207 helix: 2.50 (0.20), residues: 647 sheet: 0.26 (0.21), residues: 616 loop : -1.05 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.005 TRP A 64 HIS 0.023 0.003 HIS B 245 PHE 0.049 0.006 PHE B 464 TYR 0.050 0.005 TYR A 266 ARG 0.036 0.003 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 836 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 56 LEU cc_start: 0.8376 (tp) cc_final: 0.8147 (mt) REVERT: A 57 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.7842 (Cg_endo) REVERT: A 80 ASP cc_start: 0.8130 (t0) cc_final: 0.7835 (t70) REVERT: A 224 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8375 (pm20) REVERT: A 266 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6959 (m-80) REVERT: A 287 ASP cc_start: 0.7376 (t0) cc_final: 0.6892 (t0) REVERT: A 358 ILE cc_start: 0.7708 (mt) cc_final: 0.7053 (tp) REVERT: A 544 ASN cc_start: 0.7902 (m-40) cc_final: 0.7426 (p0) REVERT: A 732 THR cc_start: 0.8109 (p) cc_final: 0.7493 (t) REVERT: A 733 LYS cc_start: 0.8600 (mttt) cc_final: 0.7989 (mttm) REVERT: A 778 THR cc_start: 0.8196 (m) cc_final: 0.7939 (p) REVERT: A 788 ILE cc_start: 0.8117 (mm) cc_final: 0.7856 (mm) REVERT: A 866 THR cc_start: 0.5962 (p) cc_final: 0.5260 (m) REVERT: A 877 LEU cc_start: 0.8666 (mt) cc_final: 0.8291 (mm) REVERT: A 878 LEU cc_start: 0.8403 (tt) cc_final: 0.8145 (tt) REVERT: A 905 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7853 (mmm-85) REVERT: A 921 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7597 (tptp) REVERT: A 926 GLN cc_start: 0.8414 (mt0) cc_final: 0.7744 (mt0) REVERT: A 954 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6959 (tp-100) REVERT: A 957 GLN cc_start: 0.8503 (tt0) cc_final: 0.8105 (tm-30) REVERT: A 964 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8177 (tptm) REVERT: A 965 GLN cc_start: 0.8548 (mm110) cc_final: 0.8250 (mm-40) REVERT: A 991 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7031 (t) REVERT: A 995 ARG cc_start: 0.8480 (ttm170) cc_final: 0.8043 (tpp80) REVERT: A 997 ILE cc_start: 0.8761 (mt) cc_final: 0.8493 (mt) REVERT: A 1014 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7735 (mmm-85) REVERT: A 1019 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6366 (tpp80) REVERT: A 1023 ASN cc_start: 0.7704 (t0) cc_final: 0.7457 (t0) REVERT: A 1038 LYS cc_start: 0.8281 (mttt) cc_final: 0.7734 (ttmm) REVERT: A 1045 LYS cc_start: 0.7576 (tttp) cc_final: 0.7178 (tttp) REVERT: A 1106 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7458 (mt0) REVERT: A 1128 VAL cc_start: 0.7931 (p) cc_final: 0.7512 (m) REVERT: B 65 PHE cc_start: 0.8460 (m-80) cc_final: 0.8006 (m-80) REVERT: B 141 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4525 (tt) REVERT: B 187 LYS cc_start: 0.8195 (tptp) cc_final: 0.7822 (ptmt) REVERT: B 220 PHE cc_start: 0.3216 (OUTLIER) cc_final: 0.1398 (t80) REVERT: B 233 ILE cc_start: 0.5802 (pt) cc_final: 0.3982 (mt) REVERT: B 266 TYR cc_start: 0.6351 (m-10) cc_final: 0.5724 (m-10) REVERT: B 289 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.8016 (p) REVERT: B 293 LEU cc_start: 0.8513 (tp) cc_final: 0.8193 (tt) REVERT: B 378 LYS cc_start: 0.6964 (ptmm) cc_final: 0.6738 (ttpp) REVERT: B 398 ASP cc_start: 0.6972 (m-30) cc_final: 0.6393 (m-30) REVERT: B 454 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.7895 (ttm-80) REVERT: B 471 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: B 533 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8112 (tp) REVERT: B 613 GLN cc_start: 0.6543 (OUTLIER) cc_final: 0.5413 (tp40) REVERT: B 714 ILE cc_start: 0.8592 (mt) cc_final: 0.8359 (mp) REVERT: B 752 LEU cc_start: 0.8771 (mm) cc_final: 0.8492 (mm) REVERT: B 776 LYS cc_start: 0.8689 (tptp) cc_final: 0.8304 (tptp) REVERT: B 779 GLN cc_start: 0.7953 (tp40) cc_final: 0.7610 (tm-30) REVERT: B 814 LYS cc_start: 0.7180 (mmtt) cc_final: 0.6900 (mmtt) REVERT: B 858 LEU cc_start: 0.7823 (mt) cc_final: 0.7588 (pp) REVERT: B 870 ILE cc_start: 0.8219 (mt) cc_final: 0.7979 (tt) REVERT: B 902 MET cc_start: 0.6910 (mmm) cc_final: 0.6600 (mmm) REVERT: B 905 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7757 (mmt-90) REVERT: B 926 GLN cc_start: 0.8312 (mt0) cc_final: 0.7864 (tp40) REVERT: B 949 GLN cc_start: 0.7841 (tp40) cc_final: 0.7634 (tp-100) REVERT: B 957 GLN cc_start: 0.8368 (mt0) cc_final: 0.8127 (tt0) REVERT: B 964 LYS cc_start: 0.8632 (ttmm) cc_final: 0.8154 (ttmm) REVERT: B 966 LEU cc_start: 0.8460 (tp) cc_final: 0.8251 (pp) REVERT: B 970 PHE cc_start: 0.7114 (m-80) cc_final: 0.6641 (m-80) REVERT: B 1118 ASP cc_start: 0.8215 (p0) cc_final: 0.7922 (p0) REVERT: B 1133 VAL cc_start: 0.7628 (m) cc_final: 0.7369 (p) REVERT: C 34 ARG cc_start: 0.5779 (tpp-160) cc_final: 0.5479 (mmm160) REVERT: C 55 PHE cc_start: 0.3913 (OUTLIER) cc_final: 0.3542 (m-10) REVERT: C 66 HIS cc_start: 0.6937 (m170) cc_final: 0.5588 (m170) REVERT: C 96 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6017 (mm-30) REVERT: C 206 LYS cc_start: 0.7266 (tptm) cc_final: 0.6909 (tptm) REVERT: C 212 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7122 (mp) REVERT: C 235 ILE cc_start: 0.8503 (mt) cc_final: 0.7989 (mt) REVERT: C 276 LEU cc_start: 0.5838 (tp) cc_final: 0.5039 (tp) REVERT: C 277 LEU cc_start: 0.7204 (mt) cc_final: 0.6730 (mt) REVERT: C 308 VAL cc_start: 0.7258 (t) cc_final: 0.6989 (p) REVERT: C 370 ASN cc_start: 0.8169 (t0) cc_final: 0.7833 (t0) REVERT: C 377 PHE cc_start: 0.7694 (t80) cc_final: 0.7493 (t80) REVERT: C 406 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: C 436 TRP cc_start: 0.7329 (p-90) cc_final: 0.6927 (p-90) REVERT: C 440 ASN cc_start: 0.8834 (m-40) cc_final: 0.8243 (p0) REVERT: C 463 PRO cc_start: 0.6203 (Cg_endo) cc_final: 0.6001 (Cg_exo) REVERT: C 559 PHE cc_start: 0.7908 (m-10) cc_final: 0.7374 (m-80) REVERT: C 563 GLN cc_start: 0.7940 (mt0) cc_final: 0.7655 (mt0) REVERT: C 581 THR cc_start: 0.7540 (m) cc_final: 0.7182 (m) REVERT: C 588 THR cc_start: 0.6637 (OUTLIER) cc_final: 0.6071 (t) REVERT: C 611 LEU cc_start: 0.4993 (OUTLIER) cc_final: 0.4730 (tt) REVERT: C 618 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 642 VAL cc_start: 0.8824 (m) cc_final: 0.8590 (p) REVERT: C 655 HIS cc_start: 0.8946 (OUTLIER) cc_final: 0.8263 (p90) REVERT: C 657 ASN cc_start: 0.7928 (m-40) cc_final: 0.7555 (t0) REVERT: C 727 LEU cc_start: 0.8013 (mt) cc_final: 0.7766 (mt) REVERT: C 752 LEU cc_start: 0.8861 (mp) cc_final: 0.7905 (mm) REVERT: C 773 GLU cc_start: 0.8000 (tt0) cc_final: 0.7033 (tt0) REVERT: C 776 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8580 (ttpt) REVERT: C 824 ASN cc_start: 0.9195 (m110) cc_final: 0.8833 (p0) REVERT: C 877 LEU cc_start: 0.8683 (mt) cc_final: 0.8258 (mt) REVERT: C 878 LEU cc_start: 0.8525 (mt) cc_final: 0.8142 (mt) REVERT: C 901 GLN cc_start: 0.8015 (tt0) cc_final: 0.7562 (tt0) REVERT: C 905 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7248 (tpp80) REVERT: C 918 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 920 GLN cc_start: 0.8221 (tt0) cc_final: 0.7982 (tt0) REVERT: C 921 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: C 925 ASN cc_start: 0.8366 (m-40) cc_final: 0.8150 (m-40) REVERT: C 926 GLN cc_start: 0.8790 (mt0) cc_final: 0.8167 (mt0) REVERT: C 1013 ILE cc_start: 0.8644 (mt) cc_final: 0.8102 (mm) REVERT: C 1017 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 1021 SER cc_start: 0.8867 (t) cc_final: 0.8560 (p) REVERT: C 1083 HIS cc_start: 0.4829 (OUTLIER) cc_final: 0.4453 (t-90) REVERT: C 1092 GLU cc_start: 0.4282 (OUTLIER) cc_final: 0.3718 (pp20) outliers start: 211 outliers final: 75 residues processed: 981 average time/residue: 0.3981 time to fit residues: 601.8681 Evaluate side-chains 790 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 691 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.5980 chunk 244 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 146 HIS A 245 HIS ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 690 GLN A 755 GLN A 764 ASN A 774 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 928 ASN ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1002 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN B 165 ASN B 207 HIS B 211 ASN B 245 HIS B 334 ASN B 370 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 641 ASN B 644 GLN B 764 ASN B 777 ASN B 928 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 245 HIS C 317 ASN C 321 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 644 GLN C 655 HIS C 762 GLN C 824 ASN C 856 ASN C 928 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 26536 Z= 0.287 Angle : 0.846 16.604 36139 Z= 0.420 Chirality : 0.058 1.109 4208 Planarity : 0.006 0.115 4627 Dihedral : 9.778 104.725 4420 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 0.36 % Allowed : 5.06 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3207 helix: 1.69 (0.20), residues: 657 sheet: 0.15 (0.20), residues: 646 loop : -1.07 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 64 HIS 0.015 0.002 HIS C 655 PHE 0.036 0.003 PHE B 559 TYR 0.024 0.002 TYR C 453 ARG 0.039 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 786 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7895 (t-90) cc_final: 0.7685 (t-90) REVERT: A 80 ASP cc_start: 0.8247 (t0) cc_final: 0.7867 (t70) REVERT: A 224 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8390 (pm20) REVERT: A 298 GLU cc_start: 0.8178 (tt0) cc_final: 0.7729 (tt0) REVERT: A 342 PHE cc_start: 0.9118 (m-10) cc_final: 0.8624 (m-10) REVERT: A 436 TRP cc_start: 0.7680 (p90) cc_final: 0.7275 (t60) REVERT: A 437 ASN cc_start: 0.7937 (t0) cc_final: 0.7624 (t0) REVERT: A 532 ASN cc_start: 0.8111 (t0) cc_final: 0.7840 (t0) REVERT: A 567 ARG cc_start: 0.6769 (ptp-110) cc_final: 0.6445 (ttp-110) REVERT: A 571 ASP cc_start: 0.6586 (t0) cc_final: 0.6241 (t0) REVERT: A 574 ASP cc_start: 0.6234 (p0) cc_final: 0.4603 (t0) REVERT: A 658 ASN cc_start: 0.7370 (t0) cc_final: 0.7136 (t0) REVERT: A 733 LYS cc_start: 0.8408 (mttt) cc_final: 0.7943 (mttt) REVERT: A 751 ASN cc_start: 0.8203 (m110) cc_final: 0.7990 (m110) REVERT: A 762 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7635 (mm-40) REVERT: A 765 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7575 (ttp-170) REVERT: A 773 GLU cc_start: 0.8615 (tt0) cc_final: 0.8145 (tt0) REVERT: A 778 THR cc_start: 0.8455 (m) cc_final: 0.8133 (p) REVERT: A 796 ASP cc_start: 0.7662 (m-30) cc_final: 0.7387 (m-30) REVERT: A 878 LEU cc_start: 0.8474 (tt) cc_final: 0.8240 (tp) REVERT: A 902 MET cc_start: 0.7230 (tpp) cc_final: 0.7022 (tpp) REVERT: A 905 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8306 (mtt180) REVERT: A 919 ASN cc_start: 0.8936 (m110) cc_final: 0.8621 (m110) REVERT: A 921 LYS cc_start: 0.8446 (mmtt) cc_final: 0.7951 (tptp) REVERT: A 926 GLN cc_start: 0.8295 (mt0) cc_final: 0.7681 (mt0) REVERT: A 928 ASN cc_start: 0.8057 (m-40) cc_final: 0.7758 (m-40) REVERT: A 933 LYS cc_start: 0.9072 (mttm) cc_final: 0.8389 (mmmm) REVERT: A 957 GLN cc_start: 0.8579 (tt0) cc_final: 0.8072 (tm-30) REVERT: A 964 LYS cc_start: 0.8728 (mttt) cc_final: 0.8315 (tptp) REVERT: A 991 VAL cc_start: 0.7657 (p) cc_final: 0.6904 (t) REVERT: A 993 ILE cc_start: 0.8789 (mt) cc_final: 0.8526 (mm) REVERT: A 995 ARG cc_start: 0.8386 (ttm170) cc_final: 0.8045 (tpp80) REVERT: A 1009 THR cc_start: 0.7689 (m) cc_final: 0.7429 (m) REVERT: A 1014 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7645 (mmm-85) REVERT: A 1023 ASN cc_start: 0.7781 (t0) cc_final: 0.7421 (t0) REVERT: A 1036 GLN cc_start: 0.6856 (tt0) cc_final: 0.6401 (tt0) REVERT: A 1064 HIS cc_start: 0.7397 (m170) cc_final: 0.7000 (m170) REVERT: A 1077 THR cc_start: 0.7695 (t) cc_final: 0.7429 (t) REVERT: A 1102 TRP cc_start: 0.6722 (m100) cc_final: 0.6511 (m100) REVERT: B 43 PHE cc_start: 0.7304 (p90) cc_final: 0.6476 (p90) REVERT: B 52 GLN cc_start: 0.8066 (mp10) cc_final: 0.7823 (mp10) REVERT: B 65 PHE cc_start: 0.8360 (m-80) cc_final: 0.7610 (m-80) REVERT: B 91 TYR cc_start: 0.8006 (t80) cc_final: 0.7656 (t80) REVERT: B 224 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7907 (pm20) REVERT: B 277 LEU cc_start: 0.7707 (mm) cc_final: 0.7402 (mm) REVERT: B 293 LEU cc_start: 0.8632 (tp) cc_final: 0.8371 (tt) REVERT: B 331 ASN cc_start: 0.7472 (t0) cc_final: 0.6880 (m-40) REVERT: B 380 TYR cc_start: 0.7750 (m-80) cc_final: 0.7505 (m-80) REVERT: B 398 ASP cc_start: 0.6641 (m-30) cc_final: 0.5899 (m-30) REVERT: B 409 GLN cc_start: 0.8724 (mt0) cc_final: 0.8183 (mt0) REVERT: B 418 ILE cc_start: 0.8504 (mp) cc_final: 0.8267 (mp) REVERT: B 439 ASN cc_start: 0.7996 (p0) cc_final: 0.7733 (t0) REVERT: B 509 ARG cc_start: 0.6829 (tmm160) cc_final: 0.6541 (mmm160) REVERT: B 529 LYS cc_start: 0.7548 (mmtm) cc_final: 0.7169 (ttmm) REVERT: B 535 LYS cc_start: 0.8021 (tppp) cc_final: 0.7723 (tppt) REVERT: B 557 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7447 (mtmm) REVERT: B 578 ASP cc_start: 0.7960 (p0) cc_final: 0.7683 (p0) REVERT: B 583 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7735 (tp30) REVERT: B 714 ILE cc_start: 0.8714 (mt) cc_final: 0.8458 (mp) REVERT: B 727 LEU cc_start: 0.7867 (mt) cc_final: 0.7049 (mt) REVERT: B 756 TYR cc_start: 0.7850 (m-80) cc_final: 0.7423 (m-80) REVERT: B 758 SER cc_start: 0.8026 (t) cc_final: 0.7506 (m) REVERT: B 762 GLN cc_start: 0.7730 (pp30) cc_final: 0.7314 (pp30) REVERT: B 776 LYS cc_start: 0.8540 (tptp) cc_final: 0.8069 (tptp) REVERT: B 779 GLN cc_start: 0.8055 (tp40) cc_final: 0.7625 (tp-100) REVERT: B 780 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6721 (tp30) REVERT: B 814 LYS cc_start: 0.7286 (mmtt) cc_final: 0.7002 (mmtt) REVERT: B 818 ILE cc_start: 0.8538 (mt) cc_final: 0.8327 (tp) REVERT: B 860 VAL cc_start: 0.8346 (t) cc_final: 0.8101 (p) REVERT: B 902 MET cc_start: 0.6549 (mmm) cc_final: 0.6181 (mmm) REVERT: B 905 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7755 (mmm-85) REVERT: B 909 ILE cc_start: 0.7506 (pt) cc_final: 0.6956 (mm) REVERT: B 917 TYR cc_start: 0.7501 (m-80) cc_final: 0.6911 (m-80) REVERT: B 926 GLN cc_start: 0.8137 (mt0) cc_final: 0.7843 (tp40) REVERT: B 934 ILE cc_start: 0.8406 (mm) cc_final: 0.8166 (mm) REVERT: B 935 GLN cc_start: 0.8587 (tt0) cc_final: 0.8019 (tm-30) REVERT: B 949 GLN cc_start: 0.8002 (tp40) cc_final: 0.7785 (tp40) REVERT: B 955 ASN cc_start: 0.8388 (m110) cc_final: 0.7696 (m110) REVERT: B 964 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8306 (ttmm) REVERT: B 991 VAL cc_start: 0.8809 (m) cc_final: 0.8391 (t) REVERT: B 994 ASP cc_start: 0.7927 (t0) cc_final: 0.7561 (t0) REVERT: B 1001 LEU cc_start: 0.8642 (mt) cc_final: 0.8382 (mt) REVERT: B 1003 SER cc_start: 0.8631 (m) cc_final: 0.8353 (p) REVERT: B 1028 LYS cc_start: 0.7859 (tppt) cc_final: 0.6998 (tppt) REVERT: B 1034 LEU cc_start: 0.7437 (mt) cc_final: 0.7204 (mt) REVERT: B 1111 GLU cc_start: 0.6742 (pp20) cc_final: 0.6109 (pm20) REVERT: C 43 PHE cc_start: 0.7223 (t80) cc_final: 0.6232 (t80) REVERT: C 65 PHE cc_start: 0.8782 (m-80) cc_final: 0.8356 (m-80) REVERT: C 99 ASN cc_start: 0.8247 (m110) cc_final: 0.7759 (m-40) REVERT: C 104 TRP cc_start: 0.5262 (m-90) cc_final: 0.4763 (m-90) REVERT: C 203 ILE cc_start: 0.8166 (tt) cc_final: 0.7891 (tp) REVERT: C 237 ARG cc_start: 0.8523 (ptm-80) cc_final: 0.8171 (mtm110) REVERT: C 241 LEU cc_start: 0.8078 (mp) cc_final: 0.7877 (mm) REVERT: C 277 LEU cc_start: 0.7589 (mt) cc_final: 0.7230 (mt) REVERT: C 356 LYS cc_start: 0.7074 (ttmm) cc_final: 0.6239 (ttpp) REVERT: C 370 ASN cc_start: 0.7741 (t0) cc_final: 0.7470 (t0) REVERT: C 440 ASN cc_start: 0.8784 (m-40) cc_final: 0.8138 (p0) REVERT: C 533 LEU cc_start: 0.8593 (tp) cc_final: 0.8284 (tp) REVERT: C 535 LYS cc_start: 0.8013 (mttt) cc_final: 0.7796 (mtmm) REVERT: C 583 GLU cc_start: 0.8412 (mp0) cc_final: 0.8088 (mp0) REVERT: C 657 ASN cc_start: 0.7968 (m-40) cc_final: 0.7762 (m-40) REVERT: C 693 ILE cc_start: 0.7857 (pt) cc_final: 0.7576 (mp) REVERT: C 699 LEU cc_start: 0.8195 (pt) cc_final: 0.7875 (pt) REVERT: C 710 ASN cc_start: 0.8058 (p0) cc_final: 0.7803 (m-40) REVERT: C 727 LEU cc_start: 0.8198 (mt) cc_final: 0.7823 (mt) REVERT: C 730 SER cc_start: 0.6971 (p) cc_final: 0.6692 (t) REVERT: C 731 MET cc_start: 0.7972 (ptt) cc_final: 0.7663 (ptt) REVERT: C 740 MET cc_start: 0.6591 (tpp) cc_final: 0.6343 (tpp) REVERT: C 763 LEU cc_start: 0.8711 (mt) cc_final: 0.8446 (mt) REVERT: C 776 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8547 (ttpt) REVERT: C 778 THR cc_start: 0.8842 (m) cc_final: 0.8553 (p) REVERT: C 866 THR cc_start: 0.6928 (p) cc_final: 0.6064 (p) REVERT: C 877 LEU cc_start: 0.8675 (mt) cc_final: 0.8436 (mt) REVERT: C 878 LEU cc_start: 0.8566 (mt) cc_final: 0.8320 (mt) REVERT: C 905 ARG cc_start: 0.8265 (mtt-85) cc_final: 0.7737 (tpp80) REVERT: C 918 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7801 (mt-10) REVERT: C 921 LYS cc_start: 0.8827 (mmpt) cc_final: 0.8441 (mtpp) REVERT: C 926 GLN cc_start: 0.8381 (mt0) cc_final: 0.7923 (mt0) REVERT: C 949 GLN cc_start: 0.7989 (tp-100) cc_final: 0.7564 (tp-100) REVERT: C 953 ASN cc_start: 0.8559 (m-40) cc_final: 0.8260 (m-40) REVERT: C 964 LYS cc_start: 0.8512 (tttt) cc_final: 0.8170 (mtpt) REVERT: C 965 GLN cc_start: 0.8108 (tp40) cc_final: 0.7502 (tp-100) REVERT: C 1013 ILE cc_start: 0.8810 (mt) cc_final: 0.8289 (mm) REVERT: C 1014 ARG cc_start: 0.7421 (mtt90) cc_final: 0.7137 (ptp-110) REVERT: C 1017 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7744 (mt-10) REVERT: C 1029 MET cc_start: 0.7297 (tpp) cc_final: 0.7045 (tpp) REVERT: C 1061 VAL cc_start: 0.7719 (t) cc_final: 0.7517 (m) REVERT: C 1084 ASP cc_start: 0.6145 (m-30) cc_final: 0.5856 (m-30) outliers start: 10 outliers final: 2 residues processed: 793 average time/residue: 0.4171 time to fit residues: 508.0339 Evaluate side-chains 683 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 681 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 293 optimal weight: 7.9990 chunk 317 optimal weight: 2.9990 chunk 261 optimal weight: 20.0000 chunk 291 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 235 optimal weight: 0.0030 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 409 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26536 Z= 0.262 Angle : 0.755 13.470 36139 Z= 0.379 Chirality : 0.053 0.684 4208 Planarity : 0.005 0.098 4627 Dihedral : 9.526 103.505 4420 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.05 % Favored : 95.92 % Rotamer: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3207 helix: 1.16 (0.20), residues: 675 sheet: -0.06 (0.20), residues: 635 loop : -1.12 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 436 HIS 0.012 0.002 HIS B 66 PHE 0.024 0.002 PHE B 823 TYR 0.022 0.002 TYR B 365 ARG 0.013 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 767 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6506 (ttpt) REVERT: A 49 HIS cc_start: 0.7818 (t70) cc_final: 0.7523 (t-90) REVERT: A 80 ASP cc_start: 0.8399 (t0) cc_final: 0.8070 (t0) REVERT: A 298 GLU cc_start: 0.8099 (tt0) cc_final: 0.7715 (tt0) REVERT: A 342 PHE cc_start: 0.9164 (m-10) cc_final: 0.8808 (m-10) REVERT: A 374 PHE cc_start: 0.7642 (m-10) cc_final: 0.7392 (m-10) REVERT: A 532 ASN cc_start: 0.8201 (t0) cc_final: 0.7937 (t0) REVERT: A 574 ASP cc_start: 0.6316 (p0) cc_final: 0.4584 (t70) REVERT: A 643 PHE cc_start: 0.7309 (t80) cc_final: 0.7054 (t80) REVERT: A 658 ASN cc_start: 0.7587 (t0) cc_final: 0.7289 (t0) REVERT: A 733 LYS cc_start: 0.8294 (mttt) cc_final: 0.8038 (mtpt) REVERT: A 751 ASN cc_start: 0.8162 (m110) cc_final: 0.7873 (m110) REVERT: A 773 GLU cc_start: 0.8404 (tt0) cc_final: 0.7856 (tt0) REVERT: A 778 THR cc_start: 0.8483 (m) cc_final: 0.8242 (p) REVERT: A 791 THR cc_start: 0.8625 (m) cc_final: 0.8275 (m) REVERT: A 869 MET cc_start: 0.8183 (ptp) cc_final: 0.6738 (ptp) REVERT: A 870 ILE cc_start: 0.8913 (mt) cc_final: 0.8505 (mt) REVERT: A 878 LEU cc_start: 0.8414 (tt) cc_final: 0.8035 (tt) REVERT: A 905 ARG cc_start: 0.8774 (mtt-85) cc_final: 0.8301 (mtt90) REVERT: A 919 ASN cc_start: 0.8897 (m110) cc_final: 0.8671 (m110) REVERT: A 921 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8076 (tptp) REVERT: A 926 GLN cc_start: 0.8339 (mt0) cc_final: 0.7967 (mt0) REVERT: A 928 ASN cc_start: 0.8019 (m-40) cc_final: 0.7650 (m-40) REVERT: A 933 LYS cc_start: 0.9046 (mttm) cc_final: 0.8283 (mmmm) REVERT: A 957 GLN cc_start: 0.8611 (tt0) cc_final: 0.8204 (tm-30) REVERT: A 991 VAL cc_start: 0.7959 (p) cc_final: 0.7241 (t) REVERT: A 993 ILE cc_start: 0.8904 (mt) cc_final: 0.8636 (mt) REVERT: A 995 ARG cc_start: 0.8443 (ttm170) cc_final: 0.8141 (tpp80) REVERT: A 1009 THR cc_start: 0.7811 (m) cc_final: 0.7548 (p) REVERT: A 1023 ASN cc_start: 0.7760 (t0) cc_final: 0.7365 (t0) REVERT: A 1034 LEU cc_start: 0.8286 (mm) cc_final: 0.8050 (mm) REVERT: A 1036 GLN cc_start: 0.6751 (tt0) cc_final: 0.6364 (tt0) REVERT: A 1038 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7820 (mttm) REVERT: A 1041 ASP cc_start: 0.7485 (t0) cc_final: 0.7252 (t0) REVERT: A 1045 LYS cc_start: 0.8669 (mppt) cc_final: 0.8333 (mmtm) REVERT: A 1064 HIS cc_start: 0.7396 (m170) cc_final: 0.6943 (m170) REVERT: A 1072 GLU cc_start: 0.8376 (pm20) cc_final: 0.8076 (pm20) REVERT: A 1109 PHE cc_start: 0.7650 (t80) cc_final: 0.7318 (t80) REVERT: B 44 ARG cc_start: 0.7604 (mtt90) cc_final: 0.7007 (mtt90) REVERT: B 54 LEU cc_start: 0.7858 (mp) cc_final: 0.7156 (tt) REVERT: B 65 PHE cc_start: 0.8418 (m-80) cc_final: 0.7660 (m-80) REVERT: B 99 ASN cc_start: 0.8316 (t0) cc_final: 0.7551 (t0) REVERT: B 227 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7433 (p) REVERT: B 293 LEU cc_start: 0.8613 (tp) cc_final: 0.7813 (tt) REVERT: B 294 ASP cc_start: 0.8066 (m-30) cc_final: 0.7528 (m-30) REVERT: B 300 LYS cc_start: 0.8851 (mttt) cc_final: 0.8406 (mttm) REVERT: B 351 TYR cc_start: 0.7093 (p90) cc_final: 0.6848 (p90) REVERT: B 353 TRP cc_start: 0.7864 (p90) cc_final: 0.6756 (p90) REVERT: B 365 TYR cc_start: 0.8010 (m-80) cc_final: 0.7677 (m-80) REVERT: B 380 TYR cc_start: 0.7846 (m-80) cc_final: 0.7580 (m-80) REVERT: B 398 ASP cc_start: 0.6569 (m-30) cc_final: 0.6279 (m-30) REVERT: B 409 GLN cc_start: 0.8861 (mt0) cc_final: 0.8177 (tt0) REVERT: B 418 ILE cc_start: 0.8670 (mp) cc_final: 0.8426 (mp) REVERT: B 439 ASN cc_start: 0.8116 (p0) cc_final: 0.7772 (t0) REVERT: B 454 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8027 (ttm170) REVERT: B 535 LYS cc_start: 0.8076 (tppp) cc_final: 0.7629 (tppt) REVERT: B 557 LYS cc_start: 0.7836 (mtmm) cc_final: 0.7317 (mtmm) REVERT: B 578 ASP cc_start: 0.8020 (p0) cc_final: 0.7814 (p0) REVERT: B 583 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8044 (tp30) REVERT: B 714 ILE cc_start: 0.8768 (mt) cc_final: 0.8447 (mm) REVERT: B 725 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7106 (tm-30) REVERT: B 756 TYR cc_start: 0.7997 (m-80) cc_final: 0.7084 (m-80) REVERT: B 758 SER cc_start: 0.8238 (t) cc_final: 0.7725 (m) REVERT: B 779 GLN cc_start: 0.8158 (tp40) cc_final: 0.7627 (tp-100) REVERT: B 780 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6708 (tp30) REVERT: B 814 LYS cc_start: 0.7321 (mmtt) cc_final: 0.7076 (mmtt) REVERT: B 823 PHE cc_start: 0.7732 (m-80) cc_final: 0.7469 (m-10) REVERT: B 860 VAL cc_start: 0.8373 (t) cc_final: 0.8121 (p) REVERT: B 902 MET cc_start: 0.6769 (mmm) cc_final: 0.6352 (mmm) REVERT: B 905 ARG cc_start: 0.8233 (mmt90) cc_final: 0.7861 (mmm-85) REVERT: B 909 ILE cc_start: 0.7781 (pt) cc_final: 0.7210 (mm) REVERT: B 917 TYR cc_start: 0.7506 (m-80) cc_final: 0.6882 (m-10) REVERT: B 926 GLN cc_start: 0.8227 (mt0) cc_final: 0.7936 (tp40) REVERT: B 934 ILE cc_start: 0.8322 (mm) cc_final: 0.8121 (mm) REVERT: B 935 GLN cc_start: 0.8599 (tt0) cc_final: 0.8010 (tm-30) REVERT: B 954 GLN cc_start: 0.7957 (pp30) cc_final: 0.7644 (pp30) REVERT: B 955 ASN cc_start: 0.8691 (m110) cc_final: 0.7990 (m110) REVERT: B 957 GLN cc_start: 0.8842 (tt0) cc_final: 0.8247 (tp40) REVERT: B 963 VAL cc_start: 0.8646 (t) cc_final: 0.8432 (p) REVERT: B 965 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7954 (tp40) REVERT: B 979 ASP cc_start: 0.8523 (t0) cc_final: 0.8276 (t0) REVERT: B 991 VAL cc_start: 0.8773 (m) cc_final: 0.8395 (t) REVERT: B 994 ASP cc_start: 0.7730 (t0) cc_final: 0.7129 (t0) REVERT: B 1001 LEU cc_start: 0.8692 (mt) cc_final: 0.8438 (mt) REVERT: B 1003 SER cc_start: 0.8591 (m) cc_final: 0.8339 (p) REVERT: B 1004 LEU cc_start: 0.8504 (mt) cc_final: 0.8268 (mt) REVERT: B 1005 GLN cc_start: 0.7728 (pp30) cc_final: 0.7489 (pp30) REVERT: B 1024 LEU cc_start: 0.8392 (tt) cc_final: 0.8079 (tt) REVERT: B 1031 GLU cc_start: 0.6453 (tt0) cc_final: 0.6017 (tt0) REVERT: B 1106 GLN cc_start: 0.7677 (tm-30) cc_final: 0.6693 (tm-30) REVERT: B 1109 PHE cc_start: 0.6965 (t80) cc_final: 0.6135 (t80) REVERT: C 65 PHE cc_start: 0.8809 (m-80) cc_final: 0.8336 (m-80) REVERT: C 104 TRP cc_start: 0.5513 (m-90) cc_final: 0.4864 (m-90) REVERT: C 129 LYS cc_start: 0.8018 (ptpp) cc_final: 0.7809 (pttm) REVERT: C 203 ILE cc_start: 0.8278 (tt) cc_final: 0.8062 (tp) REVERT: C 238 PHE cc_start: 0.8097 (p90) cc_final: 0.7178 (p90) REVERT: C 267 VAL cc_start: 0.6754 (t) cc_final: 0.6387 (t) REVERT: C 293 LEU cc_start: 0.8536 (tp) cc_final: 0.8328 (tp) REVERT: C 294 ASP cc_start: 0.8140 (p0) cc_final: 0.7913 (p0) REVERT: C 333 THR cc_start: 0.8651 (m) cc_final: 0.8334 (p) REVERT: C 370 ASN cc_start: 0.7867 (t0) cc_final: 0.7560 (t0) REVERT: C 440 ASN cc_start: 0.8794 (m-40) cc_final: 0.8113 (p0) REVERT: C 535 LYS cc_start: 0.8218 (mttt) cc_final: 0.7515 (ttmm) REVERT: C 552 LEU cc_start: 0.8186 (mm) cc_final: 0.7716 (mm) REVERT: C 557 LYS cc_start: 0.9089 (mttt) cc_final: 0.8850 (mmmt) REVERT: C 577 ARG cc_start: 0.7854 (ttm170) cc_final: 0.7305 (ttm170) REVERT: C 578 ASP cc_start: 0.7203 (t0) cc_final: 0.6860 (t0) REVERT: C 583 GLU cc_start: 0.8626 (mp0) cc_final: 0.8173 (mp0) REVERT: C 584 ILE cc_start: 0.8347 (tp) cc_final: 0.7795 (tp) REVERT: C 693 ILE cc_start: 0.7940 (pt) cc_final: 0.7638 (mp) REVERT: C 710 ASN cc_start: 0.8185 (p0) cc_final: 0.7912 (m110) REVERT: C 731 MET cc_start: 0.8055 (ptt) cc_final: 0.7832 (ptt) REVERT: C 761 THR cc_start: 0.8353 (p) cc_final: 0.7882 (t) REVERT: C 773 GLU cc_start: 0.8411 (tt0) cc_final: 0.7943 (tt0) REVERT: C 774 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7962 (mm-40) REVERT: C 776 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8469 (ttpt) REVERT: C 796 ASP cc_start: 0.8140 (m-30) cc_final: 0.7887 (m-30) REVERT: C 797 PHE cc_start: 0.7720 (m-80) cc_final: 0.6279 (m-80) REVERT: C 865 LEU cc_start: 0.8329 (mt) cc_final: 0.7754 (mt) REVERT: C 866 THR cc_start: 0.6944 (p) cc_final: 0.5942 (p) REVERT: C 878 LEU cc_start: 0.8525 (mt) cc_final: 0.8243 (mt) REVERT: C 901 GLN cc_start: 0.7765 (tt0) cc_final: 0.6881 (tm-30) REVERT: C 902 MET cc_start: 0.7686 (tmm) cc_final: 0.7464 (tmm) REVERT: C 905 ARG cc_start: 0.8312 (mtt-85) cc_final: 0.7759 (mtt-85) REVERT: C 921 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8486 (mtpp) REVERT: C 926 GLN cc_start: 0.8378 (mt0) cc_final: 0.7973 (mt0) REVERT: C 937 SER cc_start: 0.9322 (t) cc_final: 0.9065 (p) REVERT: C 949 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7673 (tm-30) REVERT: C 959 LEU cc_start: 0.8699 (tp) cc_final: 0.8470 (tp) REVERT: C 964 LYS cc_start: 0.8568 (tttt) cc_final: 0.8244 (ptpt) REVERT: C 1007 TYR cc_start: 0.8340 (t80) cc_final: 0.7712 (t80) REVERT: C 1013 ILE cc_start: 0.8922 (mt) cc_final: 0.8384 (mm) REVERT: C 1014 ARG cc_start: 0.7536 (mtt90) cc_final: 0.6633 (ttm-80) REVERT: C 1029 MET cc_start: 0.7188 (tpp) cc_final: 0.6934 (tpp) REVERT: C 1072 GLU cc_start: 0.7422 (pm20) cc_final: 0.7034 (pm20) REVERT: C 1081 ILE cc_start: 0.7647 (mt) cc_final: 0.7079 (mt) REVERT: C 1088 HIS cc_start: 0.6946 (m-70) cc_final: 0.6565 (m-70) outliers start: 1 outliers final: 0 residues processed: 768 average time/residue: 0.4003 time to fit residues: 474.6466 Evaluate side-chains 709 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 708 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 0.3980 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 chunk 294 optimal weight: 2.9990 chunk 312 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 279 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26536 Z= 0.209 Angle : 0.696 13.711 36139 Z= 0.347 Chirality : 0.050 0.634 4208 Planarity : 0.005 0.087 4627 Dihedral : 9.445 103.968 4420 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.14), residues: 3207 helix: 1.02 (0.20), residues: 669 sheet: -0.07 (0.19), residues: 643 loop : -1.14 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 436 HIS 0.010 0.001 HIS C 66 PHE 0.021 0.002 PHE A 906 TYR 0.030 0.002 TYR C 495 ARG 0.009 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 2.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7634 (t70) cc_final: 0.7280 (t-170) REVERT: A 80 ASP cc_start: 0.8454 (t0) cc_final: 0.8069 (t0) REVERT: A 177 MET cc_start: 0.4253 (mtm) cc_final: 0.2735 (mmp) REVERT: A 206 LYS cc_start: 0.7902 (ttpp) cc_final: 0.6835 (ttmt) REVERT: A 240 THR cc_start: 0.8507 (p) cc_final: 0.8275 (t) REVERT: A 271 GLN cc_start: 0.8286 (mp10) cc_final: 0.8029 (mp10) REVERT: A 273 ARG cc_start: 0.7510 (mmt180) cc_final: 0.7291 (mmt180) REVERT: A 281 GLU cc_start: 0.9035 (pm20) cc_final: 0.8569 (pm20) REVERT: A 298 GLU cc_start: 0.8139 (tt0) cc_final: 0.7733 (tt0) REVERT: A 342 PHE cc_start: 0.9208 (m-10) cc_final: 0.8868 (m-10) REVERT: A 532 ASN cc_start: 0.8213 (t0) cc_final: 0.7939 (t0) REVERT: A 533 LEU cc_start: 0.8799 (tp) cc_final: 0.8583 (tp) REVERT: A 567 ARG cc_start: 0.6597 (ptp-110) cc_final: 0.6130 (ptp-110) REVERT: A 583 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 646 ARG cc_start: 0.7635 (tpt90) cc_final: 0.7193 (tpt90) REVERT: A 658 ASN cc_start: 0.7760 (t0) cc_final: 0.7267 (t0) REVERT: A 733 LYS cc_start: 0.8233 (mttt) cc_final: 0.7921 (mtpt) REVERT: A 748 GLU cc_start: 0.7011 (pm20) cc_final: 0.5796 (mp0) REVERT: A 751 ASN cc_start: 0.8069 (m110) cc_final: 0.7745 (m110) REVERT: A 772 VAL cc_start: 0.9191 (t) cc_final: 0.8031 (m) REVERT: A 773 GLU cc_start: 0.8450 (tt0) cc_final: 0.8050 (tt0) REVERT: A 796 ASP cc_start: 0.7533 (m-30) cc_final: 0.7235 (m-30) REVERT: A 869 MET cc_start: 0.8047 (ptp) cc_final: 0.6765 (ptp) REVERT: A 870 ILE cc_start: 0.8842 (mt) cc_final: 0.8498 (mt) REVERT: A 878 LEU cc_start: 0.8378 (tt) cc_final: 0.8036 (tt) REVERT: A 884 SER cc_start: 0.8122 (p) cc_final: 0.7603 (m) REVERT: A 905 ARG cc_start: 0.8727 (mtt-85) cc_final: 0.8372 (mmt90) REVERT: A 921 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8057 (tptp) REVERT: A 926 GLN cc_start: 0.8360 (mt0) cc_final: 0.7850 (mt0) REVERT: A 928 ASN cc_start: 0.8001 (m-40) cc_final: 0.7733 (m-40) REVERT: A 933 LYS cc_start: 0.9033 (mttm) cc_final: 0.8225 (mmmm) REVERT: A 949 GLN cc_start: 0.8319 (pp30) cc_final: 0.8006 (pp30) REVERT: A 957 GLN cc_start: 0.8695 (tt0) cc_final: 0.8134 (tm-30) REVERT: A 965 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7866 (mm-40) REVERT: A 991 VAL cc_start: 0.8032 (p) cc_final: 0.7364 (t) REVERT: A 993 ILE cc_start: 0.8847 (mt) cc_final: 0.8541 (mt) REVERT: A 995 ARG cc_start: 0.8570 (ttm170) cc_final: 0.8128 (tpp80) REVERT: A 1023 ASN cc_start: 0.7765 (t0) cc_final: 0.7400 (t0) REVERT: A 1034 LEU cc_start: 0.8255 (mm) cc_final: 0.7973 (mm) REVERT: A 1036 GLN cc_start: 0.6682 (tt0) cc_final: 0.6216 (tt0) REVERT: A 1041 ASP cc_start: 0.7425 (t0) cc_final: 0.7114 (t70) REVERT: A 1045 LYS cc_start: 0.8682 (mppt) cc_final: 0.8406 (mmtm) REVERT: A 1064 HIS cc_start: 0.7383 (m170) cc_final: 0.6970 (m170) REVERT: A 1077 THR cc_start: 0.7893 (t) cc_final: 0.7556 (t) REVERT: A 1088 HIS cc_start: 0.7031 (m-70) cc_final: 0.6760 (m-70) REVERT: A 1089 PHE cc_start: 0.7034 (m-80) cc_final: 0.6607 (m-80) REVERT: A 1102 TRP cc_start: 0.7293 (m100) cc_final: 0.6886 (m100) REVERT: A 1109 PHE cc_start: 0.7664 (t80) cc_final: 0.7284 (t80) REVERT: B 43 PHE cc_start: 0.7477 (p90) cc_final: 0.6898 (p90) REVERT: B 44 ARG cc_start: 0.7806 (mtt90) cc_final: 0.6925 (mtt90) REVERT: B 65 PHE cc_start: 0.8358 (m-80) cc_final: 0.7577 (m-80) REVERT: B 92 PHE cc_start: 0.7462 (t80) cc_final: 0.6986 (t80) REVERT: B 99 ASN cc_start: 0.8362 (t0) cc_final: 0.7645 (t0) REVERT: B 192 PHE cc_start: 0.6369 (m-80) cc_final: 0.6061 (m-80) REVERT: B 207 HIS cc_start: 0.8692 (m90) cc_final: 0.8302 (m90) REVERT: B 293 LEU cc_start: 0.8564 (tp) cc_final: 0.7836 (tt) REVERT: B 294 ASP cc_start: 0.8102 (m-30) cc_final: 0.7471 (m-30) REVERT: B 300 LYS cc_start: 0.8886 (mttt) cc_final: 0.8361 (mttt) REVERT: B 354 ASN cc_start: 0.8725 (t0) cc_final: 0.7953 (p0) REVERT: B 380 TYR cc_start: 0.7761 (m-80) cc_final: 0.7477 (m-80) REVERT: B 395 VAL cc_start: 0.7883 (t) cc_final: 0.7485 (m) REVERT: B 398 ASP cc_start: 0.6682 (m-30) cc_final: 0.5932 (m-30) REVERT: B 409 GLN cc_start: 0.8851 (mt0) cc_final: 0.8172 (tt0) REVERT: B 418 ILE cc_start: 0.8670 (mp) cc_final: 0.8410 (mp) REVERT: B 439 ASN cc_start: 0.8116 (p0) cc_final: 0.7766 (t0) REVERT: B 454 ARG cc_start: 0.8469 (ttm-80) cc_final: 0.7864 (ttt90) REVERT: B 509 ARG cc_start: 0.7063 (tmm160) cc_final: 0.6697 (mmm160) REVERT: B 535 LYS cc_start: 0.8173 (tppp) cc_final: 0.7731 (tppt) REVERT: B 557 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7237 (mtmm) REVERT: B 578 ASP cc_start: 0.8042 (p0) cc_final: 0.7788 (p0) REVERT: B 714 ILE cc_start: 0.8754 (mt) cc_final: 0.8354 (mm) REVERT: B 725 GLU cc_start: 0.7341 (tm-30) cc_final: 0.6707 (tm-30) REVERT: B 727 LEU cc_start: 0.7877 (mt) cc_final: 0.7225 (mt) REVERT: B 758 SER cc_start: 0.8220 (t) cc_final: 0.7710 (m) REVERT: B 762 GLN cc_start: 0.7754 (pp30) cc_final: 0.7364 (pp30) REVERT: B 776 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8205 (tmtt) REVERT: B 779 GLN cc_start: 0.8222 (tp40) cc_final: 0.7540 (tm-30) REVERT: B 780 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6740 (tp30) REVERT: B 805 ILE cc_start: 0.8394 (mt) cc_final: 0.7938 (tp) REVERT: B 811 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8274 (mmmt) REVERT: B 814 LYS cc_start: 0.7291 (mmtt) cc_final: 0.7006 (mmtt) REVERT: B 818 ILE cc_start: 0.8584 (tp) cc_final: 0.8221 (tp) REVERT: B 823 PHE cc_start: 0.7739 (m-80) cc_final: 0.7521 (m-80) REVERT: B 860 VAL cc_start: 0.8351 (t) cc_final: 0.8053 (p) REVERT: B 878 LEU cc_start: 0.8566 (mt) cc_final: 0.8234 (tp) REVERT: B 909 ILE cc_start: 0.7826 (pt) cc_final: 0.7240 (mm) REVERT: B 917 TYR cc_start: 0.7536 (m-80) cc_final: 0.6545 (m-10) REVERT: B 926 GLN cc_start: 0.8264 (mt0) cc_final: 0.7878 (tp40) REVERT: B 934 ILE cc_start: 0.8138 (mm) cc_final: 0.7854 (mm) REVERT: B 935 GLN cc_start: 0.8617 (tt0) cc_final: 0.8108 (tm-30) REVERT: B 939 SER cc_start: 0.6593 (p) cc_final: 0.6375 (p) REVERT: B 954 GLN cc_start: 0.7906 (pp30) cc_final: 0.7603 (pp30) REVERT: B 955 ASN cc_start: 0.8712 (m110) cc_final: 0.8018 (m110) REVERT: B 957 GLN cc_start: 0.8890 (tt0) cc_final: 0.8245 (tp40) REVERT: B 965 GLN cc_start: 0.8459 (tp-100) cc_final: 0.7991 (tp-100) REVERT: B 966 LEU cc_start: 0.8794 (tp) cc_final: 0.8580 (tp) REVERT: B 970 PHE cc_start: 0.6517 (m-10) cc_final: 0.6247 (m-10) REVERT: B 979 ASP cc_start: 0.8478 (t0) cc_final: 0.8131 (t0) REVERT: B 991 VAL cc_start: 0.8738 (m) cc_final: 0.8375 (t) REVERT: B 1001 LEU cc_start: 0.8678 (mt) cc_final: 0.8339 (mt) REVERT: B 1003 SER cc_start: 0.8571 (m) cc_final: 0.8337 (p) REVERT: B 1031 GLU cc_start: 0.6506 (tt0) cc_final: 0.6080 (tt0) REVERT: B 1038 LYS cc_start: 0.8713 (tppt) cc_final: 0.8351 (tppt) REVERT: B 1113 GLN cc_start: 0.7436 (mp10) cc_final: 0.6912 (mp10) REVERT: C 65 PHE cc_start: 0.8825 (m-80) cc_final: 0.8248 (m-80) REVERT: C 99 ASN cc_start: 0.8173 (m-40) cc_final: 0.7856 (m-40) REVERT: C 104 TRP cc_start: 0.5706 (m-90) cc_final: 0.4959 (m-90) REVERT: C 238 PHE cc_start: 0.8106 (p90) cc_final: 0.7200 (p90) REVERT: C 265 TYR cc_start: 0.7460 (p90) cc_final: 0.7186 (p90) REVERT: C 293 LEU cc_start: 0.8553 (tp) cc_final: 0.8312 (tp) REVERT: C 294 ASP cc_start: 0.8137 (p0) cc_final: 0.7762 (p0) REVERT: C 357 ARG cc_start: 0.6311 (mtt180) cc_final: 0.5991 (mtt180) REVERT: C 396 TYR cc_start: 0.7821 (m-80) cc_final: 0.7094 (m-80) REVERT: C 440 ASN cc_start: 0.8729 (m-40) cc_final: 0.8043 (p0) REVERT: C 535 LYS cc_start: 0.8203 (mttt) cc_final: 0.7525 (ttmm) REVERT: C 552 LEU cc_start: 0.8295 (mm) cc_final: 0.7766 (mm) REVERT: C 557 LYS cc_start: 0.9132 (mttt) cc_final: 0.8798 (mmmt) REVERT: C 577 ARG cc_start: 0.8026 (ttm170) cc_final: 0.7257 (ttm110) REVERT: C 583 GLU cc_start: 0.8782 (mp0) cc_final: 0.8257 (mp0) REVERT: C 727 LEU cc_start: 0.8059 (mt) cc_final: 0.7722 (mt) REVERT: C 776 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8444 (ttpt) REVERT: C 796 ASP cc_start: 0.8125 (m-30) cc_final: 0.7868 (m-30) REVERT: C 797 PHE cc_start: 0.8140 (m-80) cc_final: 0.6518 (m-80) REVERT: C 808 ASP cc_start: 0.8400 (t70) cc_final: 0.8197 (t0) REVERT: C 865 LEU cc_start: 0.8319 (mt) cc_final: 0.7989 (mt) REVERT: C 878 LEU cc_start: 0.8513 (mt) cc_final: 0.8308 (mt) REVERT: C 920 GLN cc_start: 0.8122 (tt0) cc_final: 0.7903 (tt0) REVERT: C 921 LYS cc_start: 0.8726 (mmpt) cc_final: 0.8318 (mtpp) REVERT: C 925 ASN cc_start: 0.8460 (m-40) cc_final: 0.8247 (m-40) REVERT: C 926 GLN cc_start: 0.8383 (mt0) cc_final: 0.7879 (mt0) REVERT: C 949 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7903 (tm-30) REVERT: C 964 LYS cc_start: 0.8711 (tttt) cc_final: 0.8401 (mtpt) REVERT: C 1013 ILE cc_start: 0.8844 (mt) cc_final: 0.8402 (mm) REVERT: C 1017 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7871 (mt-10) REVERT: C 1081 ILE cc_start: 0.7752 (mt) cc_final: 0.7412 (mm) REVERT: C 1088 HIS cc_start: 0.6948 (m-70) cc_final: 0.6518 (m-70) REVERT: C 1110 TYR cc_start: 0.7878 (t80) cc_final: 0.7586 (t80) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 0.4304 time to fit residues: 497.5057 Evaluate side-chains 692 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 692 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 266 optimal weight: 3.9990 chunk 215 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 1.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS B 394 ASN B 422 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1054 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 26536 Z= 0.304 Angle : 0.757 12.857 36139 Z= 0.390 Chirality : 0.051 0.654 4208 Planarity : 0.005 0.097 4627 Dihedral : 9.531 102.200 4420 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3207 helix: 0.61 (0.20), residues: 672 sheet: -0.22 (0.19), residues: 658 loop : -1.31 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 436 HIS 0.013 0.002 HIS B1048 PHE 0.029 0.002 PHE A 220 TYR 0.024 0.002 TYR C 279 ARG 0.012 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 767 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7598 (t70) cc_final: 0.7263 (t70) REVERT: A 80 ASP cc_start: 0.8548 (t0) cc_final: 0.8075 (t0) REVERT: A 91 TYR cc_start: 0.7671 (t80) cc_final: 0.7392 (t80) REVERT: A 92 PHE cc_start: 0.7329 (t80) cc_final: 0.6841 (t80) REVERT: A 104 TRP cc_start: 0.7662 (m-90) cc_final: 0.6983 (m-90) REVERT: A 113 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8636 (tppt) REVERT: A 191 GLU cc_start: 0.7234 (pm20) cc_final: 0.6983 (pm20) REVERT: A 221 SER cc_start: 0.8252 (m) cc_final: 0.7789 (t) REVERT: A 240 THR cc_start: 0.8701 (p) cc_final: 0.8347 (t) REVERT: A 271 GLN cc_start: 0.8401 (mp10) cc_final: 0.8109 (mp10) REVERT: A 281 GLU cc_start: 0.9105 (pm20) cc_final: 0.8563 (pm20) REVERT: A 298 GLU cc_start: 0.8136 (tt0) cc_final: 0.7740 (tt0) REVERT: A 303 LEU cc_start: 0.8955 (tp) cc_final: 0.8662 (tp) REVERT: A 319 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7050 (mtm110) REVERT: A 342 PHE cc_start: 0.9320 (m-10) cc_final: 0.8985 (m-10) REVERT: A 532 ASN cc_start: 0.8347 (t0) cc_final: 0.8100 (t0) REVERT: A 583 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8345 (mm-30) REVERT: A 592 PHE cc_start: 0.7302 (t80) cc_final: 0.7017 (t80) REVERT: A 646 ARG cc_start: 0.7837 (tpt90) cc_final: 0.7593 (tpt90) REVERT: A 714 ILE cc_start: 0.8129 (mm) cc_final: 0.7676 (mm) REVERT: A 731 MET cc_start: 0.8121 (pmm) cc_final: 0.7888 (pmm) REVERT: A 733 LYS cc_start: 0.8410 (mttt) cc_final: 0.7923 (mtmt) REVERT: A 748 GLU cc_start: 0.7120 (pm20) cc_final: 0.6607 (mp0) REVERT: A 751 ASN cc_start: 0.8085 (m110) cc_final: 0.7717 (m110) REVERT: A 762 GLN cc_start: 0.8203 (mp10) cc_final: 0.7907 (mp10) REVERT: A 772 VAL cc_start: 0.9204 (t) cc_final: 0.7884 (m) REVERT: A 776 LYS cc_start: 0.8408 (mptt) cc_final: 0.7927 (mptt) REVERT: A 869 MET cc_start: 0.8207 (ptp) cc_final: 0.7255 (ptp) REVERT: A 870 ILE cc_start: 0.8985 (mt) cc_final: 0.8643 (mt) REVERT: A 873 TYR cc_start: 0.8000 (m-10) cc_final: 0.7701 (m-10) REVERT: A 878 LEU cc_start: 0.8365 (tt) cc_final: 0.8157 (tt) REVERT: A 884 SER cc_start: 0.8323 (p) cc_final: 0.7889 (m) REVERT: A 905 ARG cc_start: 0.8836 (mtt-85) cc_final: 0.8278 (mmt90) REVERT: A 919 ASN cc_start: 0.8933 (m110) cc_final: 0.8706 (m110) REVERT: A 921 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8334 (tptt) REVERT: A 926 GLN cc_start: 0.8535 (mt0) cc_final: 0.8231 (mt0) REVERT: A 933 LYS cc_start: 0.9115 (mttm) cc_final: 0.8355 (mmmm) REVERT: A 957 GLN cc_start: 0.8831 (tt0) cc_final: 0.8534 (tm-30) REVERT: A 964 LYS cc_start: 0.8803 (mttt) cc_final: 0.8345 (tptp) REVERT: A 973 ILE cc_start: 0.8587 (mt) cc_final: 0.8043 (tt) REVERT: A 991 VAL cc_start: 0.8356 (p) cc_final: 0.7777 (t) REVERT: A 993 ILE cc_start: 0.8880 (mt) cc_final: 0.8622 (mt) REVERT: A 995 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8264 (tpp80) REVERT: A 1023 ASN cc_start: 0.7960 (t0) cc_final: 0.7646 (t0) REVERT: A 1036 GLN cc_start: 0.6678 (tt0) cc_final: 0.6240 (tt0) REVERT: A 1038 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7919 (mttp) REVERT: A 1045 LYS cc_start: 0.8762 (mppt) cc_final: 0.8494 (mmtm) REVERT: A 1064 HIS cc_start: 0.7392 (m170) cc_final: 0.7056 (m170) REVERT: A 1088 HIS cc_start: 0.7240 (m-70) cc_final: 0.6952 (m-70) REVERT: A 1101 HIS cc_start: 0.8496 (m90) cc_final: 0.8224 (m90) REVERT: A 1102 TRP cc_start: 0.7670 (m100) cc_final: 0.7048 (m100) REVERT: A 1109 PHE cc_start: 0.7966 (t80) cc_final: 0.7575 (t80) REVERT: A 1129 VAL cc_start: 0.8057 (t) cc_final: 0.7762 (p) REVERT: B 43 PHE cc_start: 0.7660 (p90) cc_final: 0.7287 (p90) REVERT: B 44 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7265 (mtm-85) REVERT: B 65 PHE cc_start: 0.8628 (m-80) cc_final: 0.7856 (m-80) REVERT: B 92 PHE cc_start: 0.7530 (t80) cc_final: 0.6982 (t80) REVERT: B 99 ASN cc_start: 0.8420 (t0) cc_final: 0.7769 (t0) REVERT: B 192 PHE cc_start: 0.6651 (m-80) cc_final: 0.6259 (m-80) REVERT: B 206 LYS cc_start: 0.7716 (tptp) cc_final: 0.7063 (ptmm) REVERT: B 207 HIS cc_start: 0.8789 (m-70) cc_final: 0.7994 (m-70) REVERT: B 293 LEU cc_start: 0.8575 (tp) cc_final: 0.7843 (tt) REVERT: B 294 ASP cc_start: 0.8198 (m-30) cc_final: 0.7473 (m-30) REVERT: B 300 LYS cc_start: 0.8946 (mttt) cc_final: 0.8463 (mttm) REVERT: B 354 ASN cc_start: 0.8755 (t0) cc_final: 0.7796 (p0) REVERT: B 355 ARG cc_start: 0.7663 (mpt180) cc_final: 0.7224 (mpt180) REVERT: B 378 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8221 (tttm) REVERT: B 380 TYR cc_start: 0.7963 (m-80) cc_final: 0.7754 (m-80) REVERT: B 395 VAL cc_start: 0.8138 (t) cc_final: 0.7783 (m) REVERT: B 409 GLN cc_start: 0.8917 (mt0) cc_final: 0.8268 (tt0) REVERT: B 436 TRP cc_start: 0.8002 (p-90) cc_final: 0.7633 (p-90) REVERT: B 439 ASN cc_start: 0.8269 (p0) cc_final: 0.7906 (t0) REVERT: B 454 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8036 (ttp-170) REVERT: B 557 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7446 (mtmm) REVERT: B 578 ASP cc_start: 0.8259 (p0) cc_final: 0.7856 (p0) REVERT: B 583 GLU cc_start: 0.8798 (mp0) cc_final: 0.8493 (mp0) REVERT: B 712 ILE cc_start: 0.7425 (tp) cc_final: 0.6653 (tp) REVERT: B 714 ILE cc_start: 0.8730 (mt) cc_final: 0.8323 (mm) REVERT: B 725 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 762 GLN cc_start: 0.7907 (pp30) cc_final: 0.7305 (pp30) REVERT: B 763 LEU cc_start: 0.8148 (mt) cc_final: 0.7697 (mm) REVERT: B 776 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8263 (tmtt) REVERT: B 778 THR cc_start: 0.8690 (m) cc_final: 0.8263 (p) REVERT: B 779 GLN cc_start: 0.8319 (tp40) cc_final: 0.7642 (tm-30) REVERT: B 780 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6820 (tp30) REVERT: B 786 LYS cc_start: 0.7969 (mppt) cc_final: 0.7746 (mppt) REVERT: B 805 ILE cc_start: 0.8518 (mt) cc_final: 0.8263 (tp) REVERT: B 811 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8452 (mmmt) REVERT: B 902 MET cc_start: 0.7604 (mmp) cc_final: 0.7140 (tpp) REVERT: B 909 ILE cc_start: 0.7816 (pt) cc_final: 0.7402 (mm) REVERT: B 917 TYR cc_start: 0.7568 (m-10) cc_final: 0.7026 (m-10) REVERT: B 926 GLN cc_start: 0.8360 (mt0) cc_final: 0.7923 (tp40) REVERT: B 934 ILE cc_start: 0.8326 (mm) cc_final: 0.8044 (mm) REVERT: B 935 GLN cc_start: 0.8687 (tt0) cc_final: 0.8168 (tm-30) REVERT: B 954 GLN cc_start: 0.8082 (pp30) cc_final: 0.7779 (pp30) REVERT: B 955 ASN cc_start: 0.8813 (m110) cc_final: 0.8026 (m110) REVERT: B 964 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8392 (mmtm) REVERT: B 965 GLN cc_start: 0.8532 (tp-100) cc_final: 0.7997 (tp40) REVERT: B 970 PHE cc_start: 0.6713 (m-10) cc_final: 0.6240 (m-10) REVERT: B 991 VAL cc_start: 0.8944 (m) cc_final: 0.8586 (t) REVERT: B 1003 SER cc_start: 0.8741 (m) cc_final: 0.8346 (p) REVERT: B 1004 LEU cc_start: 0.8595 (mt) cc_final: 0.8066 (mt) REVERT: B 1005 GLN cc_start: 0.8013 (pp30) cc_final: 0.7763 (pp30) REVERT: B 1028 LYS cc_start: 0.8498 (tppt) cc_final: 0.7998 (tppt) REVERT: B 1031 GLU cc_start: 0.6981 (tt0) cc_final: 0.6559 (tt0) REVERT: B 1033 VAL cc_start: 0.7566 (t) cc_final: 0.7243 (t) REVERT: B 1038 LYS cc_start: 0.8775 (tppt) cc_final: 0.8396 (tppt) REVERT: B 1050 MET cc_start: 0.6739 (ptp) cc_final: 0.6511 (ptp) REVERT: B 1073 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7499 (mmtm) REVERT: B 1077 THR cc_start: 0.7794 (t) cc_final: 0.7550 (t) REVERT: B 1106 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7530 (tm-30) REVERT: B 1109 PHE cc_start: 0.7482 (t80) cc_final: 0.7079 (t80) REVERT: C 64 TRP cc_start: 0.7668 (t-100) cc_final: 0.7452 (t-100) REVERT: C 65 PHE cc_start: 0.8854 (m-80) cc_final: 0.8065 (m-80) REVERT: C 104 TRP cc_start: 0.6041 (m-90) cc_final: 0.5158 (m-90) REVERT: C 238 PHE cc_start: 0.8181 (p90) cc_final: 0.7888 (p90) REVERT: C 265 TYR cc_start: 0.7469 (p90) cc_final: 0.7134 (p90) REVERT: C 267 VAL cc_start: 0.6947 (t) cc_final: 0.6016 (t) REVERT: C 290 ASP cc_start: 0.5740 (t0) cc_final: 0.5453 (t0) REVERT: C 293 LEU cc_start: 0.8645 (tp) cc_final: 0.8313 (tp) REVERT: C 294 ASP cc_start: 0.8320 (p0) cc_final: 0.7969 (p0) REVERT: C 370 ASN cc_start: 0.8810 (m-40) cc_final: 0.8276 (p0) REVERT: C 396 TYR cc_start: 0.7960 (m-80) cc_final: 0.7206 (m-10) REVERT: C 440 ASN cc_start: 0.8756 (m-40) cc_final: 0.8070 (p0) REVERT: C 535 LYS cc_start: 0.8452 (mttt) cc_final: 0.7779 (ttmm) REVERT: C 552 LEU cc_start: 0.8397 (mm) cc_final: 0.7613 (mm) REVERT: C 554 GLU cc_start: 0.8454 (tt0) cc_final: 0.8253 (tt0) REVERT: C 557 LYS cc_start: 0.9212 (mttt) cc_final: 0.8820 (mmmt) REVERT: C 559 PHE cc_start: 0.8103 (m-10) cc_final: 0.7735 (m-10) REVERT: C 577 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7525 (ttm170) REVERT: C 578 ASP cc_start: 0.8170 (t0) cc_final: 0.7654 (t70) REVERT: C 581 THR cc_start: 0.8733 (m) cc_final: 0.8023 (m) REVERT: C 583 GLU cc_start: 0.8977 (mp0) cc_final: 0.8528 (mp0) REVERT: C 613 GLN cc_start: 0.7350 (pp30) cc_final: 0.6931 (tm-30) REVERT: C 693 ILE cc_start: 0.7857 (mp) cc_final: 0.7584 (tt) REVERT: C 727 LEU cc_start: 0.8067 (mt) cc_final: 0.7824 (mt) REVERT: C 751 ASN cc_start: 0.8528 (p0) cc_final: 0.8194 (p0) REVERT: C 752 LEU cc_start: 0.8825 (mt) cc_final: 0.8596 (mt) REVERT: C 755 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8463 (mm-40) REVERT: C 759 PHE cc_start: 0.7748 (m-80) cc_final: 0.7490 (m-10) REVERT: C 763 LEU cc_start: 0.8757 (mt) cc_final: 0.8527 (mt) REVERT: C 773 GLU cc_start: 0.8350 (tt0) cc_final: 0.7941 (tt0) REVERT: C 776 LYS cc_start: 0.8922 (ttpt) cc_final: 0.8573 (ttpt) REVERT: C 790 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8313 (mmtm) REVERT: C 796 ASP cc_start: 0.8328 (m-30) cc_final: 0.7778 (t0) REVERT: C 808 ASP cc_start: 0.8410 (t70) cc_final: 0.8152 (t0) REVERT: C 865 LEU cc_start: 0.8382 (mt) cc_final: 0.8004 (mt) REVERT: C 877 LEU cc_start: 0.8641 (mt) cc_final: 0.8427 (mt) REVERT: C 878 LEU cc_start: 0.8671 (mt) cc_final: 0.8465 (mt) REVERT: C 901 GLN cc_start: 0.8036 (tt0) cc_final: 0.7217 (tm-30) REVERT: C 902 MET cc_start: 0.8278 (tmm) cc_final: 0.7909 (tmm) REVERT: C 909 ILE cc_start: 0.8148 (pt) cc_final: 0.7502 (mm) REVERT: C 921 LYS cc_start: 0.8724 (mmpt) cc_final: 0.8320 (mttm) REVERT: C 926 GLN cc_start: 0.8557 (mt0) cc_final: 0.8089 (mt0) REVERT: C 948 LEU cc_start: 0.8854 (tt) cc_final: 0.8641 (tp) REVERT: C 953 ASN cc_start: 0.8615 (m-40) cc_final: 0.8209 (m-40) REVERT: C 964 LYS cc_start: 0.8841 (tttt) cc_final: 0.8573 (mtpt) REVERT: C 965 GLN cc_start: 0.8418 (mm110) cc_final: 0.8111 (mm-40) REVERT: C 992 GLN cc_start: 0.7894 (pp30) cc_final: 0.7615 (pp30) REVERT: C 1013 ILE cc_start: 0.8973 (mt) cc_final: 0.8511 (mm) REVERT: C 1014 ARG cc_start: 0.7680 (mtt90) cc_final: 0.6795 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7904 (mt-10) REVERT: C 1081 ILE cc_start: 0.8138 (mt) cc_final: 0.7563 (mm) REVERT: C 1088 HIS cc_start: 0.7219 (m-70) cc_final: 0.6485 (m-70) REVERT: C 1110 TYR cc_start: 0.8011 (t80) cc_final: 0.7800 (t80) outliers start: 1 outliers final: 1 residues processed: 767 average time/residue: 0.4077 time to fit residues: 482.0901 Evaluate side-chains 710 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 709 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 105 optimal weight: 0.6980 chunk 281 optimal weight: 2.9990 chunk 61 optimal weight: 0.0770 chunk 183 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 312 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 317 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 925 ASN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26536 Z= 0.200 Angle : 0.676 12.602 36139 Z= 0.337 Chirality : 0.050 0.625 4208 Planarity : 0.005 0.073 4627 Dihedral : 9.239 99.038 4420 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3207 helix: 0.90 (0.20), residues: 663 sheet: -0.10 (0.19), residues: 666 loop : -1.28 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 436 HIS 0.008 0.001 HIS B1048 PHE 0.021 0.002 PHE B 559 TYR 0.019 0.002 TYR A 917 ARG 0.010 0.001 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 749 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 HIS cc_start: 0.7547 (t70) cc_final: 0.7293 (t70) REVERT: A 80 ASP cc_start: 0.8352 (t0) cc_final: 0.7836 (t0) REVERT: A 177 MET cc_start: 0.4296 (mtm) cc_final: 0.2689 (mmp) REVERT: A 221 SER cc_start: 0.8072 (m) cc_final: 0.7618 (t) REVERT: A 273 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7393 (mmt-90) REVERT: A 281 GLU cc_start: 0.9095 (pm20) cc_final: 0.8657 (pm20) REVERT: A 298 GLU cc_start: 0.8017 (tt0) cc_final: 0.7620 (tt0) REVERT: A 303 LEU cc_start: 0.8864 (tp) cc_final: 0.8567 (tp) REVERT: A 319 ARG cc_start: 0.7405 (mtm110) cc_final: 0.7021 (mtm110) REVERT: A 532 ASN cc_start: 0.8264 (t0) cc_final: 0.7980 (t0) REVERT: A 574 ASP cc_start: 0.6324 (p0) cc_final: 0.4442 (t70) REVERT: A 583 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 592 PHE cc_start: 0.7085 (t80) cc_final: 0.6876 (t80) REVERT: A 658 ASN cc_start: 0.7840 (t0) cc_final: 0.7487 (t0) REVERT: A 733 LYS cc_start: 0.8396 (mttt) cc_final: 0.7887 (mtmt) REVERT: A 751 ASN cc_start: 0.7985 (m110) cc_final: 0.7595 (m110) REVERT: A 772 VAL cc_start: 0.9096 (t) cc_final: 0.7778 (m) REVERT: A 776 LYS cc_start: 0.8389 (mptt) cc_final: 0.7848 (mptt) REVERT: A 818 ILE cc_start: 0.9113 (mt) cc_final: 0.8874 (mt) REVERT: A 869 MET cc_start: 0.8088 (ptp) cc_final: 0.6863 (ptp) REVERT: A 870 ILE cc_start: 0.8788 (mt) cc_final: 0.8480 (mt) REVERT: A 878 LEU cc_start: 0.8181 (tt) cc_final: 0.7910 (tt) REVERT: A 884 SER cc_start: 0.8235 (p) cc_final: 0.7805 (m) REVERT: A 902 MET cc_start: 0.7180 (ttp) cc_final: 0.6526 (tmm) REVERT: A 905 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8287 (mtt90) REVERT: A 919 ASN cc_start: 0.8813 (m110) cc_final: 0.8297 (m110) REVERT: A 920 GLN cc_start: 0.8305 (pm20) cc_final: 0.8094 (pm20) REVERT: A 921 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8092 (tptp) REVERT: A 926 GLN cc_start: 0.8475 (mt0) cc_final: 0.8065 (mt0) REVERT: A 928 ASN cc_start: 0.8025 (m-40) cc_final: 0.7660 (m-40) REVERT: A 933 LYS cc_start: 0.9005 (mttm) cc_final: 0.8198 (mmmm) REVERT: A 949 GLN cc_start: 0.8371 (pp30) cc_final: 0.8040 (pp30) REVERT: A 957 GLN cc_start: 0.8741 (tt0) cc_final: 0.8189 (tm-30) REVERT: A 964 LYS cc_start: 0.8697 (mttt) cc_final: 0.8220 (tptp) REVERT: A 991 VAL cc_start: 0.8301 (p) cc_final: 0.7748 (t) REVERT: A 993 ILE cc_start: 0.8767 (mt) cc_final: 0.8476 (mt) REVERT: A 995 ARG cc_start: 0.8624 (ttm170) cc_final: 0.8215 (tpp80) REVERT: A 1005 GLN cc_start: 0.7574 (tp-100) cc_final: 0.7217 (tm-30) REVERT: A 1017 GLU cc_start: 0.8168 (tt0) cc_final: 0.7964 (tt0) REVERT: A 1038 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7806 (mttp) REVERT: A 1041 ASP cc_start: 0.7479 (t0) cc_final: 0.7159 (t0) REVERT: A 1045 LYS cc_start: 0.8772 (mppt) cc_final: 0.8536 (mmtm) REVERT: A 1064 HIS cc_start: 0.7376 (m170) cc_final: 0.6936 (m170) REVERT: A 1088 HIS cc_start: 0.7206 (m-70) cc_final: 0.6819 (m-70) REVERT: A 1101 HIS cc_start: 0.8275 (m90) cc_final: 0.8068 (m90) REVERT: A 1102 TRP cc_start: 0.7434 (m100) cc_final: 0.7095 (m100) REVERT: A 1109 PHE cc_start: 0.7833 (t80) cc_final: 0.7449 (t80) REVERT: A 1111 GLU cc_start: 0.6561 (tt0) cc_final: 0.6251 (tt0) REVERT: A 1129 VAL cc_start: 0.8044 (t) cc_final: 0.7823 (p) REVERT: B 43 PHE cc_start: 0.7392 (p90) cc_final: 0.6655 (p90) REVERT: B 44 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7396 (mpt-90) REVERT: B 65 PHE cc_start: 0.8503 (m-80) cc_final: 0.7736 (m-80) REVERT: B 92 PHE cc_start: 0.7393 (t80) cc_final: 0.6903 (t80) REVERT: B 99 ASN cc_start: 0.8405 (t0) cc_final: 0.7720 (t0) REVERT: B 192 PHE cc_start: 0.6521 (m-80) cc_final: 0.6199 (m-80) REVERT: B 207 HIS cc_start: 0.8756 (m-70) cc_final: 0.8208 (m-70) REVERT: B 293 LEU cc_start: 0.8507 (tp) cc_final: 0.7737 (tt) REVERT: B 294 ASP cc_start: 0.8058 (m-30) cc_final: 0.7373 (m-30) REVERT: B 300 LYS cc_start: 0.8888 (mttt) cc_final: 0.8376 (mttm) REVERT: B 304 LYS cc_start: 0.9159 (mppt) cc_final: 0.8677 (mmtm) REVERT: B 354 ASN cc_start: 0.8655 (t0) cc_final: 0.7737 (p0) REVERT: B 355 ARG cc_start: 0.7554 (mpt180) cc_final: 0.7207 (mpt180) REVERT: B 395 VAL cc_start: 0.8056 (t) cc_final: 0.7705 (m) REVERT: B 409 GLN cc_start: 0.8849 (mt0) cc_final: 0.8158 (tt0) REVERT: B 418 ILE cc_start: 0.8688 (mp) cc_final: 0.8450 (mp) REVERT: B 439 ASN cc_start: 0.8254 (p0) cc_final: 0.7896 (t0) REVERT: B 454 ARG cc_start: 0.8515 (ttm-80) cc_final: 0.8059 (ttp-170) REVERT: B 557 LYS cc_start: 0.7845 (mtmm) cc_final: 0.7298 (mtmm) REVERT: B 578 ASP cc_start: 0.8045 (p0) cc_final: 0.7564 (p0) REVERT: B 583 GLU cc_start: 0.8762 (mp0) cc_final: 0.8287 (mp0) REVERT: B 585 LEU cc_start: 0.8857 (mt) cc_final: 0.8318 (tt) REVERT: B 712 ILE cc_start: 0.7368 (tp) cc_final: 0.6657 (tp) REVERT: B 714 ILE cc_start: 0.8566 (mt) cc_final: 0.8215 (mm) REVERT: B 740 MET cc_start: 0.9358 (tpt) cc_final: 0.8869 (tpt) REVERT: B 741 TYR cc_start: 0.7872 (t80) cc_final: 0.7510 (t80) REVERT: B 762 GLN cc_start: 0.7758 (pp30) cc_final: 0.7101 (pp30) REVERT: B 763 LEU cc_start: 0.8045 (mt) cc_final: 0.7582 (mm) REVERT: B 770 ILE cc_start: 0.8302 (mt) cc_final: 0.8090 (mt) REVERT: B 776 LYS cc_start: 0.8490 (tmtt) cc_final: 0.8128 (tmtt) REVERT: B 778 THR cc_start: 0.8558 (m) cc_final: 0.8191 (p) REVERT: B 779 GLN cc_start: 0.8215 (tp40) cc_final: 0.7573 (tm-30) REVERT: B 780 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6650 (tp30) REVERT: B 786 LYS cc_start: 0.7908 (mppt) cc_final: 0.7704 (mppt) REVERT: B 805 ILE cc_start: 0.8477 (mt) cc_final: 0.8212 (tp) REVERT: B 811 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8396 (mmmt) REVERT: B 894 LEU cc_start: 0.8416 (mm) cc_final: 0.8182 (mm) REVERT: B 902 MET cc_start: 0.7361 (mmp) cc_final: 0.6862 (mmp) REVERT: B 909 ILE cc_start: 0.7714 (pt) cc_final: 0.7161 (mm) REVERT: B 917 TYR cc_start: 0.7517 (m-10) cc_final: 0.6981 (m-10) REVERT: B 926 GLN cc_start: 0.8297 (mt0) cc_final: 0.7837 (tp40) REVERT: B 934 ILE cc_start: 0.8191 (mm) cc_final: 0.7908 (mm) REVERT: B 935 GLN cc_start: 0.8661 (tt0) cc_final: 0.8130 (tm-30) REVERT: B 954 GLN cc_start: 0.8026 (pp30) cc_final: 0.7661 (pp30) REVERT: B 955 ASN cc_start: 0.8846 (m110) cc_final: 0.8016 (m110) REVERT: B 964 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8123 (ttmm) REVERT: B 965 GLN cc_start: 0.8291 (tp-100) cc_final: 0.7626 (tp40) REVERT: B 970 PHE cc_start: 0.6612 (m-10) cc_final: 0.6087 (m-10) REVERT: B 991 VAL cc_start: 0.8799 (m) cc_final: 0.8505 (t) REVERT: B 1004 LEU cc_start: 0.8455 (mt) cc_final: 0.8041 (mm) REVERT: B 1031 GLU cc_start: 0.6611 (tt0) cc_final: 0.6193 (tt0) REVERT: B 1033 VAL cc_start: 0.7633 (t) cc_final: 0.7173 (t) REVERT: B 1038 LYS cc_start: 0.8728 (tppt) cc_final: 0.8362 (tppt) REVERT: B 1073 LYS cc_start: 0.7615 (mtpp) cc_final: 0.7409 (mmtm) REVERT: B 1077 THR cc_start: 0.7695 (t) cc_final: 0.7455 (t) REVERT: B 1092 GLU cc_start: 0.6932 (pm20) cc_final: 0.6691 (pm20) REVERT: B 1105 THR cc_start: 0.7057 (m) cc_final: 0.6487 (m) REVERT: C 40 ASP cc_start: 0.8446 (m-30) cc_final: 0.8087 (m-30) REVERT: C 65 PHE cc_start: 0.8767 (m-80) cc_final: 0.8055 (m-80) REVERT: C 99 ASN cc_start: 0.8399 (m-40) cc_final: 0.8188 (m-40) REVERT: C 104 TRP cc_start: 0.5882 (m-90) cc_final: 0.5056 (m-90) REVERT: C 238 PHE cc_start: 0.8244 (p90) cc_final: 0.7983 (p90) REVERT: C 265 TYR cc_start: 0.7413 (p90) cc_final: 0.7160 (p90) REVERT: C 294 ASP cc_start: 0.8172 (p0) cc_final: 0.7726 (p0) REVERT: C 357 ARG cc_start: 0.5626 (mtt180) cc_final: 0.5098 (mtt180) REVERT: C 370 ASN cc_start: 0.8793 (m-40) cc_final: 0.8269 (p0) REVERT: C 377 PHE cc_start: 0.7992 (t80) cc_final: 0.7768 (t80) REVERT: C 378 LYS cc_start: 0.7657 (tptp) cc_final: 0.7206 (tptp) REVERT: C 396 TYR cc_start: 0.7635 (m-80) cc_final: 0.6999 (m-80) REVERT: C 440 ASN cc_start: 0.8639 (m-40) cc_final: 0.8065 (p0) REVERT: C 535 LYS cc_start: 0.8400 (mttt) cc_final: 0.7755 (ttmm) REVERT: C 552 LEU cc_start: 0.8268 (mm) cc_final: 0.7594 (mm) REVERT: C 554 GLU cc_start: 0.8463 (tt0) cc_final: 0.8262 (tt0) REVERT: C 557 LYS cc_start: 0.9201 (mttt) cc_final: 0.8759 (mmmt) REVERT: C 578 ASP cc_start: 0.7746 (t0) cc_final: 0.7297 (t70) REVERT: C 583 GLU cc_start: 0.8591 (mp0) cc_final: 0.8370 (mp0) REVERT: C 613 GLN cc_start: 0.7252 (pp30) cc_final: 0.6932 (tm-30) REVERT: C 693 ILE cc_start: 0.7737 (mp) cc_final: 0.7401 (tt) REVERT: C 727 LEU cc_start: 0.8046 (mt) cc_final: 0.7778 (mt) REVERT: C 759 PHE cc_start: 0.7560 (m-80) cc_final: 0.7289 (m-80) REVERT: C 773 GLU cc_start: 0.8348 (tt0) cc_final: 0.7632 (tt0) REVERT: C 775 ASP cc_start: 0.7997 (m-30) cc_final: 0.7340 (m-30) REVERT: C 776 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8303 (ttpt) REVERT: C 777 ASN cc_start: 0.8626 (m110) cc_final: 0.8341 (m110) REVERT: C 778 THR cc_start: 0.8696 (m) cc_final: 0.8440 (p) REVERT: C 790 LYS cc_start: 0.8536 (mmtm) cc_final: 0.8316 (mmtm) REVERT: C 796 ASP cc_start: 0.8612 (m-30) cc_final: 0.7803 (t0) REVERT: C 808 ASP cc_start: 0.8381 (t70) cc_final: 0.8115 (t0) REVERT: C 865 LEU cc_start: 0.8377 (mt) cc_final: 0.7935 (mt) REVERT: C 905 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7753 (tpp80) REVERT: C 909 ILE cc_start: 0.8078 (pt) cc_final: 0.7378 (mm) REVERT: C 921 LYS cc_start: 0.8557 (mmpt) cc_final: 0.8345 (mmtt) REVERT: C 926 GLN cc_start: 0.8365 (mt0) cc_final: 0.7975 (mt0) REVERT: C 948 LEU cc_start: 0.8820 (tt) cc_final: 0.8613 (tp) REVERT: C 949 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7949 (tm-30) REVERT: C 965 GLN cc_start: 0.8349 (mm110) cc_final: 0.8003 (mm-40) REVERT: C 992 GLN cc_start: 0.7875 (pp30) cc_final: 0.7620 (pp30) REVERT: C 1005 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6829 (tm-30) REVERT: C 1012 LEU cc_start: 0.9062 (mt) cc_final: 0.8790 (mt) REVERT: C 1013 ILE cc_start: 0.8918 (mt) cc_final: 0.8670 (mm) REVERT: C 1017 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7968 (mt-10) REVERT: C 1028 LYS cc_start: 0.8591 (mmtp) cc_final: 0.8345 (mmtp) REVERT: C 1081 ILE cc_start: 0.7945 (mt) cc_final: 0.7543 (mm) REVERT: C 1088 HIS cc_start: 0.7010 (m-70) cc_final: 0.6552 (m-70) REVERT: C 1109 PHE cc_start: 0.7422 (t80) cc_final: 0.6910 (t80) outliers start: 0 outliers final: 0 residues processed: 749 average time/residue: 0.4148 time to fit residues: 478.2030 Evaluate side-chains 707 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 707 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 301 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 176 optimal weight: 0.9990 chunk 263 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 311 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 143 optimal weight: 0.0000 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26536 Z= 0.246 Angle : 0.707 13.582 36139 Z= 0.357 Chirality : 0.050 0.610 4208 Planarity : 0.005 0.064 4627 Dihedral : 9.178 96.039 4420 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.02 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3207 helix: 0.83 (0.20), residues: 658 sheet: -0.16 (0.20), residues: 645 loop : -1.34 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 436 HIS 0.008 0.001 HIS B1048 PHE 0.025 0.002 PHE B 559 TYR 0.020 0.002 TYR C 741 ARG 0.010 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 734 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8553 (mmmt) cc_final: 0.7860 (mmmm) REVERT: A 49 HIS cc_start: 0.7589 (t70) cc_final: 0.6847 (t70) REVERT: A 58 PHE cc_start: 0.8255 (m-10) cc_final: 0.7878 (m-80) REVERT: A 80 ASP cc_start: 0.8440 (t0) cc_final: 0.7977 (t0) REVERT: A 177 MET cc_start: 0.4314 (mtm) cc_final: 0.2619 (mmp) REVERT: A 221 SER cc_start: 0.8227 (m) cc_final: 0.7832 (t) REVERT: A 273 ARG cc_start: 0.8352 (mmt-90) cc_final: 0.7746 (mmt-90) REVERT: A 298 GLU cc_start: 0.8004 (tt0) cc_final: 0.7568 (tt0) REVERT: A 303 LEU cc_start: 0.8909 (tp) cc_final: 0.8636 (tp) REVERT: A 342 PHE cc_start: 0.9162 (t80) cc_final: 0.8844 (t80) REVERT: A 374 PHE cc_start: 0.8099 (m-10) cc_final: 0.7717 (m-10) REVERT: A 532 ASN cc_start: 0.8356 (t0) cc_final: 0.8096 (t0) REVERT: A 558 LYS cc_start: 0.8509 (mttm) cc_final: 0.8081 (mmtt) REVERT: A 583 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8380 (mm-30) REVERT: A 658 ASN cc_start: 0.7827 (t0) cc_final: 0.7336 (t0) REVERT: A 674 TYR cc_start: 0.7372 (t80) cc_final: 0.6337 (t80) REVERT: A 690 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6046 (pm20) REVERT: A 733 LYS cc_start: 0.8432 (mttt) cc_final: 0.7699 (mtmt) REVERT: A 751 ASN cc_start: 0.8065 (m110) cc_final: 0.7649 (m110) REVERT: A 753 LEU cc_start: 0.8512 (tp) cc_final: 0.8300 (tp) REVERT: A 762 GLN cc_start: 0.8208 (mp10) cc_final: 0.7804 (mp10) REVERT: A 763 LEU cc_start: 0.8410 (mt) cc_final: 0.8164 (mt) REVERT: A 770 ILE cc_start: 0.8490 (mt) cc_final: 0.8165 (mt) REVERT: A 772 VAL cc_start: 0.9043 (t) cc_final: 0.7556 (m) REVERT: A 774 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7165 (mm-40) REVERT: A 776 LYS cc_start: 0.8362 (mptt) cc_final: 0.8046 (mptt) REVERT: A 787 GLN cc_start: 0.7763 (pm20) cc_final: 0.7420 (pp30) REVERT: A 869 MET cc_start: 0.8147 (ptp) cc_final: 0.7181 (ptp) REVERT: A 870 ILE cc_start: 0.8871 (mt) cc_final: 0.8596 (mt) REVERT: A 878 LEU cc_start: 0.8275 (tt) cc_final: 0.8002 (tt) REVERT: A 884 SER cc_start: 0.8303 (p) cc_final: 0.7964 (m) REVERT: A 905 ARG cc_start: 0.8836 (mtt-85) cc_final: 0.8254 (mtt90) REVERT: A 919 ASN cc_start: 0.8821 (m110) cc_final: 0.8477 (m110) REVERT: A 921 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8269 (tptt) REVERT: A 926 GLN cc_start: 0.8475 (mt0) cc_final: 0.8212 (mt0) REVERT: A 933 LYS cc_start: 0.9033 (mttm) cc_final: 0.8300 (mmmm) REVERT: A 949 GLN cc_start: 0.8355 (pp30) cc_final: 0.8058 (pp30) REVERT: A 957 GLN cc_start: 0.8805 (tt0) cc_final: 0.8455 (tm-30) REVERT: A 964 LYS cc_start: 0.8779 (mttt) cc_final: 0.8352 (tptp) REVERT: A 990 GLU cc_start: 0.8033 (tt0) cc_final: 0.7641 (tt0) REVERT: A 991 VAL cc_start: 0.8495 (p) cc_final: 0.7984 (t) REVERT: A 993 ILE cc_start: 0.8810 (mt) cc_final: 0.8531 (mt) REVERT: A 995 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8287 (tpp80) REVERT: A 1017 GLU cc_start: 0.8139 (tt0) cc_final: 0.7861 (tt0) REVERT: A 1023 ASN cc_start: 0.8186 (t0) cc_final: 0.7789 (t0) REVERT: A 1034 LEU cc_start: 0.8488 (mm) cc_final: 0.8219 (mm) REVERT: A 1041 ASP cc_start: 0.7574 (t0) cc_final: 0.7110 (t0) REVERT: A 1054 GLN cc_start: 0.7139 (mp10) cc_final: 0.6901 (mp10) REVERT: A 1084 ASP cc_start: 0.8422 (p0) cc_final: 0.8061 (p0) REVERT: A 1088 HIS cc_start: 0.7262 (m-70) cc_final: 0.6980 (m-70) REVERT: A 1101 HIS cc_start: 0.8353 (m90) cc_final: 0.8086 (m90) REVERT: A 1102 TRP cc_start: 0.7677 (m100) cc_final: 0.7224 (m100) REVERT: A 1109 PHE cc_start: 0.7974 (t80) cc_final: 0.7524 (t80) REVERT: B 43 PHE cc_start: 0.7606 (p90) cc_final: 0.7120 (p90) REVERT: B 44 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7703 (mtt90) REVERT: B 53 ASP cc_start: 0.7490 (t0) cc_final: 0.6930 (t0) REVERT: B 54 LEU cc_start: 0.8137 (mp) cc_final: 0.7714 (mp) REVERT: B 65 PHE cc_start: 0.8707 (m-80) cc_final: 0.7956 (m-80) REVERT: B 92 PHE cc_start: 0.7437 (t80) cc_final: 0.6943 (t80) REVERT: B 99 ASN cc_start: 0.8503 (t0) cc_final: 0.7886 (t0) REVERT: B 160 TYR cc_start: 0.7697 (p90) cc_final: 0.7490 (p90) REVERT: B 187 LYS cc_start: 0.8546 (pttm) cc_final: 0.8216 (pttm) REVERT: B 192 PHE cc_start: 0.6666 (m-80) cc_final: 0.6303 (m-80) REVERT: B 207 HIS cc_start: 0.8772 (m-70) cc_final: 0.8210 (m-70) REVERT: B 300 LYS cc_start: 0.8931 (mttt) cc_final: 0.8409 (mttt) REVERT: B 354 ASN cc_start: 0.8670 (t0) cc_final: 0.7875 (p0) REVERT: B 355 ARG cc_start: 0.7495 (mpt180) cc_final: 0.7135 (mmt180) REVERT: B 395 VAL cc_start: 0.8038 (t) cc_final: 0.7661 (m) REVERT: B 409 GLN cc_start: 0.8890 (mt0) cc_final: 0.8163 (tt0) REVERT: B 418 ILE cc_start: 0.8758 (mp) cc_final: 0.8480 (mp) REVERT: B 436 TRP cc_start: 0.8076 (p-90) cc_final: 0.7592 (p-90) REVERT: B 439 ASN cc_start: 0.8240 (p0) cc_final: 0.7839 (t0) REVERT: B 454 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8141 (ttp-170) REVERT: B 557 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7314 (mtmm) REVERT: B 583 GLU cc_start: 0.8786 (mp0) cc_final: 0.8543 (mp0) REVERT: B 712 ILE cc_start: 0.7480 (tp) cc_final: 0.6870 (tp) REVERT: B 714 ILE cc_start: 0.8603 (mt) cc_final: 0.8247 (mm) REVERT: B 722 VAL cc_start: 0.7922 (t) cc_final: 0.7688 (t) REVERT: B 756 TYR cc_start: 0.8157 (m-80) cc_final: 0.7865 (m-80) REVERT: B 776 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8140 (tmtt) REVERT: B 778 THR cc_start: 0.8689 (m) cc_final: 0.8288 (p) REVERT: B 779 GLN cc_start: 0.8276 (tp40) cc_final: 0.7622 (tm-30) REVERT: B 780 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6741 (tp30) REVERT: B 786 LYS cc_start: 0.8086 (mppt) cc_final: 0.7746 (mppt) REVERT: B 805 ILE cc_start: 0.8543 (mt) cc_final: 0.8268 (tp) REVERT: B 811 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8472 (mmmt) REVERT: B 873 TYR cc_start: 0.7726 (m-80) cc_final: 0.7185 (m-10) REVERT: B 902 MET cc_start: 0.7241 (mmp) cc_final: 0.6850 (mmp) REVERT: B 907 ASN cc_start: 0.7923 (t0) cc_final: 0.7681 (t0) REVERT: B 909 ILE cc_start: 0.7707 (pt) cc_final: 0.7264 (mm) REVERT: B 917 TYR cc_start: 0.7541 (m-10) cc_final: 0.7005 (m-10) REVERT: B 926 GLN cc_start: 0.8351 (mt0) cc_final: 0.7862 (tp40) REVERT: B 934 ILE cc_start: 0.8252 (mm) cc_final: 0.8005 (mm) REVERT: B 935 GLN cc_start: 0.8691 (tt0) cc_final: 0.8104 (tm-30) REVERT: B 954 GLN cc_start: 0.8088 (pp30) cc_final: 0.7755 (pp30) REVERT: B 955 ASN cc_start: 0.8817 (m110) cc_final: 0.7822 (m110) REVERT: B 957 GLN cc_start: 0.8974 (tt0) cc_final: 0.8341 (tp40) REVERT: B 964 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8473 (mmtm) REVERT: B 965 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7818 (tp40) REVERT: B 970 PHE cc_start: 0.6675 (m-10) cc_final: 0.5931 (m-10) REVERT: B 991 VAL cc_start: 0.8879 (m) cc_final: 0.8575 (t) REVERT: B 1004 LEU cc_start: 0.8547 (mt) cc_final: 0.8277 (mt) REVERT: B 1031 GLU cc_start: 0.6750 (tt0) cc_final: 0.6410 (tt0) REVERT: B 1033 VAL cc_start: 0.7523 (t) cc_final: 0.7063 (t) REVERT: B 1038 LYS cc_start: 0.8720 (tppt) cc_final: 0.8405 (tppt) REVERT: B 1073 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7456 (mmtm) REVERT: B 1077 THR cc_start: 0.7710 (t) cc_final: 0.7499 (t) REVERT: B 1113 GLN cc_start: 0.7782 (mp10) cc_final: 0.7349 (mp10) REVERT: C 64 TRP cc_start: 0.7643 (t-100) cc_final: 0.7420 (t-100) REVERT: C 65 PHE cc_start: 0.8786 (m-80) cc_final: 0.7947 (m-80) REVERT: C 99 ASN cc_start: 0.8551 (m-40) cc_final: 0.7950 (m-40) REVERT: C 104 TRP cc_start: 0.6061 (m-90) cc_final: 0.5161 (m-90) REVERT: C 129 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7766 (pttm) REVERT: C 197 ILE cc_start: 0.7824 (pt) cc_final: 0.7399 (mm) REVERT: C 238 PHE cc_start: 0.8376 (p90) cc_final: 0.8105 (p90) REVERT: C 265 TYR cc_start: 0.7463 (p90) cc_final: 0.7163 (p90) REVERT: C 267 VAL cc_start: 0.7085 (t) cc_final: 0.6079 (t) REVERT: C 294 ASP cc_start: 0.8225 (p0) cc_final: 0.7979 (p0) REVERT: C 306 PHE cc_start: 0.7063 (m-80) cc_final: 0.6621 (m-10) REVERT: C 370 ASN cc_start: 0.8855 (m-40) cc_final: 0.8367 (p0) REVERT: C 377 PHE cc_start: 0.8081 (t80) cc_final: 0.7858 (t80) REVERT: C 378 LYS cc_start: 0.7643 (tptp) cc_final: 0.7160 (tptp) REVERT: C 396 TYR cc_start: 0.7801 (m-80) cc_final: 0.7404 (m-80) REVERT: C 440 ASN cc_start: 0.8641 (m-40) cc_final: 0.8191 (p0) REVERT: C 535 LYS cc_start: 0.8477 (mttt) cc_final: 0.7832 (ttmm) REVERT: C 552 LEU cc_start: 0.8233 (mm) cc_final: 0.7544 (mm) REVERT: C 554 GLU cc_start: 0.8505 (tt0) cc_final: 0.8298 (tt0) REVERT: C 557 LYS cc_start: 0.9259 (mttt) cc_final: 0.8906 (mmmt) REVERT: C 578 ASP cc_start: 0.8167 (t0) cc_final: 0.7844 (t0) REVERT: C 581 THR cc_start: 0.8435 (m) cc_final: 0.8136 (m) REVERT: C 583 GLU cc_start: 0.8705 (mp0) cc_final: 0.8417 (mp0) REVERT: C 613 GLN cc_start: 0.7344 (pp30) cc_final: 0.7011 (tm-30) REVERT: C 693 ILE cc_start: 0.7819 (mp) cc_final: 0.7307 (tt) REVERT: C 707 TYR cc_start: 0.7452 (t80) cc_final: 0.6459 (t80) REVERT: C 727 LEU cc_start: 0.8073 (mt) cc_final: 0.7854 (mt) REVERT: C 759 PHE cc_start: 0.7721 (m-80) cc_final: 0.7304 (m-80) REVERT: C 773 GLU cc_start: 0.8289 (tt0) cc_final: 0.7665 (tt0) REVERT: C 777 ASN cc_start: 0.8581 (m110) cc_final: 0.8304 (m110) REVERT: C 796 ASP cc_start: 0.8611 (m-30) cc_final: 0.7818 (t0) REVERT: C 808 ASP cc_start: 0.8343 (t70) cc_final: 0.8088 (t0) REVERT: C 865 LEU cc_start: 0.8372 (mt) cc_final: 0.8110 (mt) REVERT: C 878 LEU cc_start: 0.8511 (mm) cc_final: 0.8310 (mt) REVERT: C 909 ILE cc_start: 0.8132 (pt) cc_final: 0.7467 (mm) REVERT: C 921 LYS cc_start: 0.8680 (mmpt) cc_final: 0.8320 (mmtp) REVERT: C 925 ASN cc_start: 0.8571 (m110) cc_final: 0.8329 (m110) REVERT: C 926 GLN cc_start: 0.8491 (mt0) cc_final: 0.8130 (mt0) REVERT: C 948 LEU cc_start: 0.8836 (tt) cc_final: 0.8627 (tp) REVERT: C 953 ASN cc_start: 0.8520 (m-40) cc_final: 0.8155 (m-40) REVERT: C 964 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8228 (mtmm) REVERT: C 965 GLN cc_start: 0.8464 (mm110) cc_final: 0.8148 (mm-40) REVERT: C 1012 LEU cc_start: 0.9051 (mt) cc_final: 0.8777 (mt) REVERT: C 1014 ARG cc_start: 0.7497 (mtt90) cc_final: 0.7114 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 1081 ILE cc_start: 0.7988 (mt) cc_final: 0.7373 (mm) REVERT: C 1088 HIS cc_start: 0.7003 (m-70) cc_final: 0.6467 (m-70) outliers start: 0 outliers final: 0 residues processed: 734 average time/residue: 0.4190 time to fit residues: 472.5643 Evaluate side-chains 690 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 690 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 192 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 212 optimal weight: 0.0970 chunk 153 optimal weight: 0.0370 chunk 29 optimal weight: 0.0670 chunk 244 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1002 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26536 Z= 0.189 Angle : 0.690 13.724 36139 Z= 0.340 Chirality : 0.050 0.605 4208 Planarity : 0.005 0.096 4627 Dihedral : 9.020 94.339 4420 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.76 % Rotamer: Outliers : 0.04 % Allowed : 0.78 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3207 helix: 0.84 (0.20), residues: 677 sheet: -0.12 (0.19), residues: 668 loop : -1.30 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP C 436 HIS 0.012 0.001 HIS A1048 PHE 0.019 0.001 PHE C 906 TYR 0.021 0.001 TYR C 365 ARG 0.019 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8735 (p0) cc_final: 0.8418 (p0) REVERT: A 41 LYS cc_start: 0.8570 (mmmt) cc_final: 0.8193 (mmmm) REVERT: A 49 HIS cc_start: 0.7343 (t70) cc_final: 0.6841 (t70) REVERT: A 56 LEU cc_start: 0.8480 (tp) cc_final: 0.8255 (tp) REVERT: A 80 ASP cc_start: 0.8382 (t0) cc_final: 0.7849 (t0) REVERT: A 177 MET cc_start: 0.4077 (mtm) cc_final: 0.2464 (mmp) REVERT: A 221 SER cc_start: 0.8099 (m) cc_final: 0.7686 (t) REVERT: A 273 ARG cc_start: 0.7952 (mmt-90) cc_final: 0.7387 (mmt-90) REVERT: A 298 GLU cc_start: 0.7938 (tt0) cc_final: 0.7514 (tt0) REVERT: A 303 LEU cc_start: 0.8813 (tp) cc_final: 0.8552 (tp) REVERT: A 342 PHE cc_start: 0.9027 (t80) cc_final: 0.8777 (t80) REVERT: A 374 PHE cc_start: 0.8022 (m-10) cc_final: 0.7639 (m-10) REVERT: A 532 ASN cc_start: 0.8243 (t0) cc_final: 0.7957 (t0) REVERT: A 558 LYS cc_start: 0.8483 (mttm) cc_final: 0.8052 (mmtt) REVERT: A 583 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8227 (mm-30) REVERT: A 658 ASN cc_start: 0.7885 (t0) cc_final: 0.7307 (t0) REVERT: A 674 TYR cc_start: 0.7339 (t80) cc_final: 0.6286 (t80) REVERT: A 690 GLN cc_start: 0.6733 (mm-40) cc_final: 0.6019 (pm20) REVERT: A 733 LYS cc_start: 0.8222 (mttt) cc_final: 0.7783 (mtmt) REVERT: A 751 ASN cc_start: 0.8000 (m110) cc_final: 0.7563 (m110) REVERT: A 763 LEU cc_start: 0.8428 (mt) cc_final: 0.8204 (mt) REVERT: A 770 ILE cc_start: 0.8438 (mt) cc_final: 0.8165 (mt) REVERT: A 772 VAL cc_start: 0.8920 (t) cc_final: 0.7421 (m) REVERT: A 774 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7287 (mm-40) REVERT: A 776 LYS cc_start: 0.8272 (mptt) cc_final: 0.8029 (mptt) REVERT: A 787 GLN cc_start: 0.7777 (pm20) cc_final: 0.7512 (pp30) REVERT: A 795 LYS cc_start: 0.6355 (mmpt) cc_final: 0.6001 (mptt) REVERT: A 869 MET cc_start: 0.8051 (ptp) cc_final: 0.6950 (ptp) REVERT: A 870 ILE cc_start: 0.8753 (mt) cc_final: 0.8462 (mt) REVERT: A 878 LEU cc_start: 0.8239 (tt) cc_final: 0.7848 (tt) REVERT: A 884 SER cc_start: 0.8110 (p) cc_final: 0.7736 (m) REVERT: A 887 THR cc_start: 0.5137 (p) cc_final: 0.3634 (t) REVERT: A 905 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8247 (mmt90) REVERT: A 919 ASN cc_start: 0.8670 (m110) cc_final: 0.8346 (m110) REVERT: A 921 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8227 (tptt) REVERT: A 926 GLN cc_start: 0.8383 (mt0) cc_final: 0.8092 (mt0) REVERT: A 928 ASN cc_start: 0.7993 (m-40) cc_final: 0.7578 (m-40) REVERT: A 933 LYS cc_start: 0.8986 (mttm) cc_final: 0.8204 (mmmm) REVERT: A 957 GLN cc_start: 0.8774 (tt0) cc_final: 0.7895 (tp40) REVERT: A 964 LYS cc_start: 0.8678 (mttt) cc_final: 0.8327 (tptp) REVERT: A 990 GLU cc_start: 0.7946 (tt0) cc_final: 0.7557 (tt0) REVERT: A 991 VAL cc_start: 0.8443 (p) cc_final: 0.7985 (t) REVERT: A 993 ILE cc_start: 0.8795 (mt) cc_final: 0.8499 (mt) REVERT: A 995 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8151 (tpp80) REVERT: A 1017 GLU cc_start: 0.8026 (tt0) cc_final: 0.7556 (tt0) REVERT: A 1023 ASN cc_start: 0.8138 (t0) cc_final: 0.7724 (t0) REVERT: A 1041 ASP cc_start: 0.7457 (t0) cc_final: 0.7200 (t0) REVERT: A 1045 LYS cc_start: 0.8832 (mppt) cc_final: 0.8538 (mmtm) REVERT: A 1073 LYS cc_start: 0.7332 (mmmt) cc_final: 0.7083 (mmmm) REVERT: A 1088 HIS cc_start: 0.7230 (m-70) cc_final: 0.7000 (m-70) REVERT: A 1101 HIS cc_start: 0.8122 (m90) cc_final: 0.7825 (m90) REVERT: A 1109 PHE cc_start: 0.7869 (t80) cc_final: 0.7421 (t80) REVERT: A 1129 VAL cc_start: 0.8028 (t) cc_final: 0.7806 (p) REVERT: B 43 PHE cc_start: 0.7484 (p90) cc_final: 0.7054 (p90) REVERT: B 44 ARG cc_start: 0.7949 (mtt90) cc_final: 0.7404 (mtm-85) REVERT: B 53 ASP cc_start: 0.7585 (t0) cc_final: 0.7002 (t0) REVERT: B 54 LEU cc_start: 0.8215 (mp) cc_final: 0.7796 (mp) REVERT: B 65 PHE cc_start: 0.8588 (m-80) cc_final: 0.7942 (m-80) REVERT: B 92 PHE cc_start: 0.7385 (t80) cc_final: 0.6911 (t80) REVERT: B 99 ASN cc_start: 0.8441 (t0) cc_final: 0.7771 (t0) REVERT: B 153 MET cc_start: 0.7756 (ppp) cc_final: 0.7480 (ppp) REVERT: B 187 LYS cc_start: 0.8484 (pttm) cc_final: 0.8254 (pttm) REVERT: B 192 PHE cc_start: 0.6532 (m-80) cc_final: 0.6195 (m-80) REVERT: B 206 LYS cc_start: 0.7452 (tptp) cc_final: 0.6927 (pttt) REVERT: B 207 HIS cc_start: 0.8686 (m-70) cc_final: 0.7469 (m-70) REVERT: B 300 LYS cc_start: 0.8822 (mttt) cc_final: 0.8213 (mttm) REVERT: B 354 ASN cc_start: 0.8628 (t0) cc_final: 0.7689 (p0) REVERT: B 380 TYR cc_start: 0.7503 (m-80) cc_final: 0.6985 (m-80) REVERT: B 395 VAL cc_start: 0.8027 (t) cc_final: 0.7653 (m) REVERT: B 409 GLN cc_start: 0.8846 (mt0) cc_final: 0.8138 (tt0) REVERT: B 418 ILE cc_start: 0.8648 (mp) cc_final: 0.8330 (mp) REVERT: B 439 ASN cc_start: 0.8137 (p0) cc_final: 0.7794 (t0) REVERT: B 454 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.7997 (ttt90) REVERT: B 557 LYS cc_start: 0.7607 (mtmm) cc_final: 0.7151 (mtmm) REVERT: B 577 ARG cc_start: 0.7571 (ttt180) cc_final: 0.7188 (ttt180) REVERT: B 582 LEU cc_start: 0.9017 (mt) cc_final: 0.8493 (mt) REVERT: B 583 GLU cc_start: 0.8680 (mp0) cc_final: 0.8204 (mp0) REVERT: B 585 LEU cc_start: 0.8949 (mm) cc_final: 0.8275 (tt) REVERT: B 712 ILE cc_start: 0.7330 (tp) cc_final: 0.6689 (tp) REVERT: B 714 ILE cc_start: 0.8460 (mt) cc_final: 0.8206 (mm) REVERT: B 722 VAL cc_start: 0.7963 (t) cc_final: 0.7745 (t) REVERT: B 776 LYS cc_start: 0.8454 (tmtt) cc_final: 0.8041 (tmtt) REVERT: B 778 THR cc_start: 0.8594 (m) cc_final: 0.8251 (p) REVERT: B 779 GLN cc_start: 0.8201 (tp40) cc_final: 0.7568 (tm-30) REVERT: B 780 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6607 (tp30) REVERT: B 786 LYS cc_start: 0.7951 (mppt) cc_final: 0.7689 (mppt) REVERT: B 805 ILE cc_start: 0.8471 (mt) cc_final: 0.8201 (tp) REVERT: B 811 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8455 (mmmt) REVERT: B 864 LEU cc_start: 0.8440 (tp) cc_final: 0.8138 (tp) REVERT: B 870 ILE cc_start: 0.8287 (mt) cc_final: 0.8064 (tt) REVERT: B 902 MET cc_start: 0.7367 (mmp) cc_final: 0.6919 (tpp) REVERT: B 909 ILE cc_start: 0.7655 (pt) cc_final: 0.7190 (mm) REVERT: B 917 TYR cc_start: 0.7452 (m-10) cc_final: 0.6927 (m-10) REVERT: B 926 GLN cc_start: 0.8248 (mt0) cc_final: 0.7781 (tp40) REVERT: B 934 ILE cc_start: 0.8123 (mm) cc_final: 0.7890 (mm) REVERT: B 954 GLN cc_start: 0.8002 (pp30) cc_final: 0.7658 (pp30) REVERT: B 955 ASN cc_start: 0.8858 (m110) cc_final: 0.7950 (m110) REVERT: B 957 GLN cc_start: 0.8945 (tt0) cc_final: 0.8129 (tp40) REVERT: B 964 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8357 (mmtm) REVERT: B 965 GLN cc_start: 0.8099 (tp-100) cc_final: 0.7703 (tp40) REVERT: B 970 PHE cc_start: 0.6574 (m-10) cc_final: 0.6066 (m-10) REVERT: B 991 VAL cc_start: 0.8809 (m) cc_final: 0.8504 (t) REVERT: B 1004 LEU cc_start: 0.8449 (mt) cc_final: 0.8229 (mt) REVERT: B 1031 GLU cc_start: 0.6343 (tt0) cc_final: 0.5947 (tt0) REVERT: B 1033 VAL cc_start: 0.7585 (t) cc_final: 0.7135 (t) REVERT: B 1038 LYS cc_start: 0.8695 (tppt) cc_final: 0.8312 (tppt) REVERT: B 1077 THR cc_start: 0.7664 (t) cc_final: 0.7414 (t) REVERT: B 1109 PHE cc_start: 0.7509 (t80) cc_final: 0.7253 (t80) REVERT: B 1110 TYR cc_start: 0.7902 (t80) cc_final: 0.7686 (t80) REVERT: C 64 TRP cc_start: 0.7510 (t-100) cc_final: 0.7306 (t-100) REVERT: C 65 PHE cc_start: 0.8728 (m-80) cc_final: 0.7873 (m-80) REVERT: C 99 ASN cc_start: 0.8140 (m-40) cc_final: 0.7864 (m-40) REVERT: C 104 TRP cc_start: 0.5944 (m-90) cc_final: 0.5081 (m-90) REVERT: C 129 LYS cc_start: 0.7935 (ptpp) cc_final: 0.7711 (pttm) REVERT: C 238 PHE cc_start: 0.8330 (p90) cc_final: 0.8086 (p90) REVERT: C 265 TYR cc_start: 0.7335 (p90) cc_final: 0.7036 (p90) REVERT: C 267 VAL cc_start: 0.7101 (t) cc_final: 0.5933 (t) REVERT: C 370 ASN cc_start: 0.8812 (m-40) cc_final: 0.8311 (p0) REVERT: C 377 PHE cc_start: 0.8055 (t80) cc_final: 0.7815 (t80) REVERT: C 378 LYS cc_start: 0.7662 (tptp) cc_final: 0.7151 (tptp) REVERT: C 440 ASN cc_start: 0.8549 (m-40) cc_final: 0.8108 (p0) REVERT: C 535 LYS cc_start: 0.8421 (mttt) cc_final: 0.7823 (ttmm) REVERT: C 554 GLU cc_start: 0.8448 (tt0) cc_final: 0.8242 (tt0) REVERT: C 557 LYS cc_start: 0.9242 (mttt) cc_final: 0.8896 (mmmt) REVERT: C 578 ASP cc_start: 0.7940 (t0) cc_final: 0.7210 (t70) REVERT: C 583 GLU cc_start: 0.8619 (mp0) cc_final: 0.8284 (mp0) REVERT: C 693 ILE cc_start: 0.7691 (mp) cc_final: 0.7258 (mp) REVERT: C 763 LEU cc_start: 0.8519 (mt) cc_final: 0.8228 (mt) REVERT: C 773 GLU cc_start: 0.8220 (tt0) cc_final: 0.7573 (tt0) REVERT: C 774 GLN cc_start: 0.7421 (pp30) cc_final: 0.7045 (pp30) REVERT: C 775 ASP cc_start: 0.8357 (m-30) cc_final: 0.7924 (m-30) REVERT: C 777 ASN cc_start: 0.8545 (m110) cc_final: 0.8304 (m110) REVERT: C 790 LYS cc_start: 0.8897 (mptt) cc_final: 0.8480 (mmtm) REVERT: C 796 ASP cc_start: 0.8532 (m-30) cc_final: 0.7808 (t0) REVERT: C 808 ASP cc_start: 0.8285 (t70) cc_final: 0.8028 (t0) REVERT: C 865 LEU cc_start: 0.8279 (mt) cc_final: 0.7766 (mt) REVERT: C 866 THR cc_start: 0.6819 (p) cc_final: 0.5571 (p) REVERT: C 869 MET cc_start: 0.7719 (mtm) cc_final: 0.7254 (mtm) REVERT: C 874 THR cc_start: 0.8288 (m) cc_final: 0.8079 (p) REVERT: C 909 ILE cc_start: 0.7876 (pt) cc_final: 0.7418 (mt) REVERT: C 921 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8393 (mmtp) REVERT: C 925 ASN cc_start: 0.8509 (m110) cc_final: 0.8245 (m110) REVERT: C 926 GLN cc_start: 0.8346 (mt0) cc_final: 0.7984 (mt0) REVERT: C 949 GLN cc_start: 0.8394 (tp-100) cc_final: 0.7983 (tm-30) REVERT: C 964 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8079 (mttp) REVERT: C 965 GLN cc_start: 0.8339 (mm110) cc_final: 0.7841 (mm-40) REVERT: C 1012 LEU cc_start: 0.8966 (mt) cc_final: 0.8748 (mt) REVERT: C 1014 ARG cc_start: 0.7459 (mtt90) cc_final: 0.7115 (ttm110) REVERT: C 1017 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7835 (mt-10) REVERT: C 1081 ILE cc_start: 0.7829 (mt) cc_final: 0.7600 (mm) REVERT: C 1088 HIS cc_start: 0.6969 (m-70) cc_final: 0.6479 (m-70) outliers start: 1 outliers final: 0 residues processed: 724 average time/residue: 0.4124 time to fit residues: 459.2786 Evaluate side-chains 694 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 283 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 290 optimal weight: 0.5980 chunk 174 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 262 optimal weight: 8.9990 chunk 274 optimal weight: 0.0980 chunk 289 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 437 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 613 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26536 Z= 0.225 Angle : 0.691 14.272 36139 Z= 0.346 Chirality : 0.050 0.596 4208 Planarity : 0.005 0.084 4627 Dihedral : 9.006 92.977 4420 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.05 % Favored : 94.92 % Rotamer: Outliers : 0.11 % Allowed : 0.71 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3207 helix: 0.76 (0.20), residues: 670 sheet: -0.22 (0.20), residues: 658 loop : -1.30 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 436 HIS 0.014 0.001 HIS A1048 PHE 0.025 0.002 PHE B 817 TYR 0.048 0.002 TYR A 91 ARG 0.008 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 713 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8578 (mmmt) cc_final: 0.7823 (mmmm) REVERT: A 51 THR cc_start: 0.7763 (m) cc_final: 0.7536 (t) REVERT: A 58 PHE cc_start: 0.7908 (m-80) cc_final: 0.7665 (m-10) REVERT: A 80 ASP cc_start: 0.8476 (t0) cc_final: 0.7993 (t0) REVERT: A 177 MET cc_start: 0.4088 (mtm) cc_final: 0.2391 (mmp) REVERT: A 221 SER cc_start: 0.8226 (m) cc_final: 0.7823 (t) REVERT: A 273 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7578 (mmt-90) REVERT: A 298 GLU cc_start: 0.7973 (tt0) cc_final: 0.7489 (tt0) REVERT: A 303 LEU cc_start: 0.8845 (tp) cc_final: 0.8559 (tp) REVERT: A 342 PHE cc_start: 0.9121 (t80) cc_final: 0.8833 (t80) REVERT: A 374 PHE cc_start: 0.8097 (m-10) cc_final: 0.7701 (m-10) REVERT: A 532 ASN cc_start: 0.8337 (t0) cc_final: 0.8080 (t0) REVERT: A 558 LYS cc_start: 0.8557 (mttm) cc_final: 0.8100 (mmtt) REVERT: A 583 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8344 (mm-30) REVERT: A 658 ASN cc_start: 0.7686 (t0) cc_final: 0.7451 (t0) REVERT: A 674 TYR cc_start: 0.7414 (t80) cc_final: 0.6357 (t80) REVERT: A 690 GLN cc_start: 0.6798 (mm-40) cc_final: 0.6184 (pm20) REVERT: A 733 LYS cc_start: 0.8198 (mttt) cc_final: 0.7958 (mtmt) REVERT: A 751 ASN cc_start: 0.8071 (m110) cc_final: 0.7663 (m110) REVERT: A 772 VAL cc_start: 0.8907 (t) cc_final: 0.7536 (m) REVERT: A 774 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7334 (mm-40) REVERT: A 776 LYS cc_start: 0.8320 (mptt) cc_final: 0.8041 (mptt) REVERT: A 787 GLN cc_start: 0.7894 (pm20) cc_final: 0.7566 (pp30) REVERT: A 869 MET cc_start: 0.8113 (ptp) cc_final: 0.7053 (ptp) REVERT: A 870 ILE cc_start: 0.8844 (mt) cc_final: 0.8565 (mt) REVERT: A 878 LEU cc_start: 0.8226 (tt) cc_final: 0.7894 (tt) REVERT: A 884 SER cc_start: 0.8196 (p) cc_final: 0.7850 (m) REVERT: A 887 THR cc_start: 0.5250 (p) cc_final: 0.3822 (t) REVERT: A 905 ARG cc_start: 0.8718 (mtt-85) cc_final: 0.8389 (mmt90) REVERT: A 911 VAL cc_start: 0.7865 (p) cc_final: 0.7581 (m) REVERT: A 919 ASN cc_start: 0.8697 (m110) cc_final: 0.8426 (m110) REVERT: A 921 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8339 (tptt) REVERT: A 926 GLN cc_start: 0.8427 (mt0) cc_final: 0.8168 (mt0) REVERT: A 933 LYS cc_start: 0.9032 (mttm) cc_final: 0.8250 (mmmm) REVERT: A 949 GLN cc_start: 0.8321 (pp30) cc_final: 0.8030 (pp30) REVERT: A 957 GLN cc_start: 0.8767 (tt0) cc_final: 0.8375 (tm-30) REVERT: A 964 LYS cc_start: 0.8759 (mttt) cc_final: 0.8358 (tptp) REVERT: A 990 GLU cc_start: 0.7952 (tt0) cc_final: 0.7578 (tt0) REVERT: A 991 VAL cc_start: 0.8555 (p) cc_final: 0.8110 (t) REVERT: A 995 ARG cc_start: 0.8692 (ttm170) cc_final: 0.8304 (tpp80) REVERT: A 1012 LEU cc_start: 0.8727 (pp) cc_final: 0.8156 (mm) REVERT: A 1017 GLU cc_start: 0.8083 (tt0) cc_final: 0.7794 (tt0) REVERT: A 1023 ASN cc_start: 0.8171 (t0) cc_final: 0.7796 (t0) REVERT: A 1028 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8233 (mtpp) REVERT: A 1041 ASP cc_start: 0.7491 (t0) cc_final: 0.7214 (t0) REVERT: A 1045 LYS cc_start: 0.8878 (mppt) cc_final: 0.8617 (mmtm) REVERT: A 1073 LYS cc_start: 0.7421 (mmmt) cc_final: 0.7185 (mmmm) REVERT: A 1077 THR cc_start: 0.8096 (t) cc_final: 0.7851 (t) REVERT: A 1088 HIS cc_start: 0.7359 (m-70) cc_final: 0.7057 (m-70) REVERT: A 1101 HIS cc_start: 0.8105 (m90) cc_final: 0.7870 (m-70) REVERT: A 1102 TRP cc_start: 0.7828 (m100) cc_final: 0.7419 (m100) REVERT: A 1109 PHE cc_start: 0.7902 (t80) cc_final: 0.7527 (t80) REVERT: B 43 PHE cc_start: 0.7664 (p90) cc_final: 0.7147 (p90) REVERT: B 44 ARG cc_start: 0.8016 (mtt90) cc_final: 0.7734 (mtt90) REVERT: B 53 ASP cc_start: 0.7557 (t0) cc_final: 0.7018 (t0) REVERT: B 54 LEU cc_start: 0.8197 (mp) cc_final: 0.7747 (mp) REVERT: B 65 PHE cc_start: 0.8782 (m-80) cc_final: 0.8061 (m-80) REVERT: B 92 PHE cc_start: 0.7423 (t80) cc_final: 0.7221 (t80) REVERT: B 99 ASN cc_start: 0.8482 (t0) cc_final: 0.7735 (t0) REVERT: B 187 LYS cc_start: 0.8617 (pttm) cc_final: 0.8383 (pttm) REVERT: B 190 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7818 (mmt90) REVERT: B 300 LYS cc_start: 0.8841 (mttt) cc_final: 0.8264 (mttm) REVERT: B 354 ASN cc_start: 0.8663 (t0) cc_final: 0.7931 (p0) REVERT: B 395 VAL cc_start: 0.8028 (t) cc_final: 0.7612 (m) REVERT: B 403 ARG cc_start: 0.8678 (mmt180) cc_final: 0.8380 (mmt180) REVERT: B 409 GLN cc_start: 0.8922 (mt0) cc_final: 0.8188 (tt0) REVERT: B 418 ILE cc_start: 0.8709 (mp) cc_final: 0.8368 (mp) REVERT: B 436 TRP cc_start: 0.7994 (p-90) cc_final: 0.7788 (p-90) REVERT: B 439 ASN cc_start: 0.8195 (p0) cc_final: 0.7888 (t0) REVERT: B 454 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8041 (ttt90) REVERT: B 557 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7218 (mtmm) REVERT: B 577 ARG cc_start: 0.7671 (ttt180) cc_final: 0.7269 (ttt180) REVERT: B 582 LEU cc_start: 0.8988 (mt) cc_final: 0.8443 (mt) REVERT: B 583 GLU cc_start: 0.8720 (mp0) cc_final: 0.8276 (mp0) REVERT: B 585 LEU cc_start: 0.8923 (mm) cc_final: 0.8294 (tt) REVERT: B 714 ILE cc_start: 0.8514 (mt) cc_final: 0.8285 (mm) REVERT: B 722 VAL cc_start: 0.8041 (t) cc_final: 0.7823 (t) REVERT: B 758 SER cc_start: 0.8431 (t) cc_final: 0.7964 (m) REVERT: B 776 LYS cc_start: 0.8479 (tmtt) cc_final: 0.8060 (tmtt) REVERT: B 778 THR cc_start: 0.8670 (m) cc_final: 0.8317 (p) REVERT: B 779 GLN cc_start: 0.8304 (tp40) cc_final: 0.7662 (tm-30) REVERT: B 780 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6722 (tp30) REVERT: B 786 LYS cc_start: 0.8029 (mppt) cc_final: 0.7733 (mppt) REVERT: B 805 ILE cc_start: 0.8458 (mt) cc_final: 0.8176 (tp) REVERT: B 811 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8483 (mmmt) REVERT: B 864 LEU cc_start: 0.8471 (tp) cc_final: 0.8166 (tp) REVERT: B 870 ILE cc_start: 0.8398 (mt) cc_final: 0.8090 (tt) REVERT: B 902 MET cc_start: 0.7336 (mmp) cc_final: 0.6948 (tpp) REVERT: B 909 ILE cc_start: 0.7724 (pt) cc_final: 0.7250 (mm) REVERT: B 917 TYR cc_start: 0.7605 (m-10) cc_final: 0.6975 (m-10) REVERT: B 926 GLN cc_start: 0.8153 (mt0) cc_final: 0.7598 (tp40) REVERT: B 934 ILE cc_start: 0.8132 (mm) cc_final: 0.7855 (mm) REVERT: B 935 GLN cc_start: 0.8787 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 954 GLN cc_start: 0.8055 (pp30) cc_final: 0.7794 (pp30) REVERT: B 955 ASN cc_start: 0.8866 (m110) cc_final: 0.7947 (m110) REVERT: B 957 GLN cc_start: 0.8967 (tt0) cc_final: 0.8127 (tp40) REVERT: B 964 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8437 (mmtm) REVERT: B 965 GLN cc_start: 0.8217 (tp-100) cc_final: 0.7861 (tp40) REVERT: B 970 PHE cc_start: 0.6587 (m-10) cc_final: 0.6025 (m-10) REVERT: B 991 VAL cc_start: 0.8867 (m) cc_final: 0.8591 (t) REVERT: B 1001 LEU cc_start: 0.8633 (mt) cc_final: 0.8369 (mt) REVERT: B 1004 LEU cc_start: 0.8554 (mt) cc_final: 0.8309 (mt) REVERT: B 1031 GLU cc_start: 0.6354 (tt0) cc_final: 0.5962 (tt0) REVERT: B 1033 VAL cc_start: 0.7590 (t) cc_final: 0.7380 (t) REVERT: B 1038 LYS cc_start: 0.8683 (tppt) cc_final: 0.8370 (tppt) REVERT: B 1073 LYS cc_start: 0.7528 (mmtm) cc_final: 0.7170 (mmtm) REVERT: C 47 VAL cc_start: 0.8876 (m) cc_final: 0.8539 (t) REVERT: C 64 TRP cc_start: 0.7602 (t-100) cc_final: 0.7362 (t-100) REVERT: C 65 PHE cc_start: 0.8758 (m-80) cc_final: 0.7872 (m-80) REVERT: C 99 ASN cc_start: 0.8270 (m-40) cc_final: 0.8041 (m-40) REVERT: C 104 TRP cc_start: 0.6113 (m-90) cc_final: 0.5187 (m-90) REVERT: C 238 PHE cc_start: 0.8418 (p90) cc_final: 0.8158 (p90) REVERT: C 265 TYR cc_start: 0.7407 (p90) cc_final: 0.7103 (p90) REVERT: C 267 VAL cc_start: 0.7197 (t) cc_final: 0.6169 (t) REVERT: C 370 ASN cc_start: 0.8881 (m-40) cc_final: 0.8372 (p0) REVERT: C 378 LYS cc_start: 0.7680 (tptp) cc_final: 0.7247 (tptp) REVERT: C 440 ASN cc_start: 0.8561 (m-40) cc_final: 0.8108 (p0) REVERT: C 535 LYS cc_start: 0.8506 (mttt) cc_final: 0.7870 (ttmm) REVERT: C 554 GLU cc_start: 0.8497 (tt0) cc_final: 0.8275 (tt0) REVERT: C 557 LYS cc_start: 0.9279 (mttt) cc_final: 0.8916 (mmmt) REVERT: C 563 GLN cc_start: 0.8236 (mt0) cc_final: 0.7748 (tm-30) REVERT: C 577 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7222 (ttm110) REVERT: C 581 THR cc_start: 0.8355 (m) cc_final: 0.7956 (m) REVERT: C 583 GLU cc_start: 0.8737 (mp0) cc_final: 0.8413 (mp0) REVERT: C 763 LEU cc_start: 0.8642 (mt) cc_final: 0.8388 (mt) REVERT: C 777 ASN cc_start: 0.8615 (m110) cc_final: 0.8181 (m110) REVERT: C 790 LYS cc_start: 0.8855 (mptt) cc_final: 0.8460 (mmtm) REVERT: C 796 ASP cc_start: 0.8580 (m-30) cc_final: 0.7858 (t0) REVERT: C 808 ASP cc_start: 0.8255 (t70) cc_final: 0.8023 (t0) REVERT: C 859 THR cc_start: 0.7894 (p) cc_final: 0.7674 (p) REVERT: C 865 LEU cc_start: 0.8279 (mt) cc_final: 0.7753 (mt) REVERT: C 866 THR cc_start: 0.6744 (p) cc_final: 0.5708 (p) REVERT: C 909 ILE cc_start: 0.7930 (pt) cc_final: 0.7455 (mt) REVERT: C 921 LYS cc_start: 0.8718 (mmpt) cc_final: 0.8368 (mmtp) REVERT: C 925 ASN cc_start: 0.8534 (m110) cc_final: 0.8321 (m110) REVERT: C 926 GLN cc_start: 0.8494 (mt0) cc_final: 0.8112 (mt0) REVERT: C 953 ASN cc_start: 0.8518 (m110) cc_final: 0.8172 (m110) REVERT: C 964 LYS cc_start: 0.8776 (mtpt) cc_final: 0.8242 (mttp) REVERT: C 965 GLN cc_start: 0.8527 (mm110) cc_final: 0.8140 (mm-40) REVERT: C 1005 GLN cc_start: 0.7789 (tp40) cc_final: 0.7242 (tp40) REVERT: C 1012 LEU cc_start: 0.9033 (mt) cc_final: 0.8749 (mm) REVERT: C 1014 ARG cc_start: 0.7686 (mtt90) cc_final: 0.7295 (ttm-80) REVERT: C 1017 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 1072 GLU cc_start: 0.8134 (pm20) cc_final: 0.7499 (pm20) REVERT: C 1081 ILE cc_start: 0.7940 (mt) cc_final: 0.7526 (mm) REVERT: C 1088 HIS cc_start: 0.6975 (m-70) cc_final: 0.6454 (m-70) outliers start: 3 outliers final: 0 residues processed: 714 average time/residue: 0.4126 time to fit residues: 454.1619 Evaluate side-chains 676 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 676 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 190 optimal weight: 2.9990 chunk 306 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 321 optimal weight: 5.9990 chunk 296 optimal weight: 0.6980 chunk 256 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26536 Z= 0.245 Angle : 0.717 15.739 36139 Z= 0.361 Chirality : 0.051 0.572 4208 Planarity : 0.005 0.095 4627 Dihedral : 9.061 89.562 4420 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 0.04 % Allowed : 0.36 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.14), residues: 3207 helix: 0.58 (0.20), residues: 671 sheet: -0.26 (0.20), residues: 641 loop : -1.36 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 436 HIS 0.016 0.001 HIS A1048 PHE 0.022 0.002 PHE C 906 TYR 0.033 0.002 TYR A 91 ARG 0.013 0.001 ARG A1039 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6414 Ramachandran restraints generated. 3207 Oldfield, 0 Emsley, 3207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 717 time to evaluate : 2.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "CYS C 617 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8596 (mmmt) cc_final: 0.7846 (mmmm) REVERT: A 51 THR cc_start: 0.7693 (m) cc_final: 0.7448 (t) REVERT: A 80 ASP cc_start: 0.8514 (t0) cc_final: 0.7986 (t0) REVERT: A 177 MET cc_start: 0.4079 (mtm) cc_final: 0.2358 (mmp) REVERT: A 221 SER cc_start: 0.8236 (m) cc_final: 0.7865 (t) REVERT: A 241 LEU cc_start: 0.7937 (mt) cc_final: 0.7331 (tt) REVERT: A 273 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.7839 (mmt-90) REVERT: A 298 GLU cc_start: 0.7945 (tt0) cc_final: 0.7409 (tt0) REVERT: A 303 LEU cc_start: 0.8857 (tp) cc_final: 0.8597 (tp) REVERT: A 342 PHE cc_start: 0.9152 (t80) cc_final: 0.8876 (t80) REVERT: A 374 PHE cc_start: 0.8188 (m-10) cc_final: 0.7799 (m-10) REVERT: A 558 LYS cc_start: 0.8666 (mttm) cc_final: 0.8202 (mmtt) REVERT: A 583 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 658 ASN cc_start: 0.7926 (t0) cc_final: 0.7319 (t0) REVERT: A 674 TYR cc_start: 0.7461 (t80) cc_final: 0.6374 (t80) REVERT: A 690 GLN cc_start: 0.6817 (mm-40) cc_final: 0.6340 (pm20) REVERT: A 733 LYS cc_start: 0.8266 (mttt) cc_final: 0.7935 (mtpt) REVERT: A 751 ASN cc_start: 0.8065 (m110) cc_final: 0.7673 (m110) REVERT: A 772 VAL cc_start: 0.8864 (t) cc_final: 0.7444 (m) REVERT: A 774 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7296 (mm-40) REVERT: A 776 LYS cc_start: 0.8347 (mptt) cc_final: 0.8081 (mptt) REVERT: A 787 GLN cc_start: 0.8011 (pm20) cc_final: 0.7714 (pp30) REVERT: A 795 LYS cc_start: 0.6607 (mmtt) cc_final: 0.6221 (mmtm) REVERT: A 869 MET cc_start: 0.8122 (ptp) cc_final: 0.7385 (ptp) REVERT: A 870 ILE cc_start: 0.8844 (mt) cc_final: 0.8643 (mt) REVERT: A 878 LEU cc_start: 0.8216 (tt) cc_final: 0.7834 (tt) REVERT: A 905 ARG cc_start: 0.8757 (mtt-85) cc_final: 0.8406 (mmt90) REVERT: A 911 VAL cc_start: 0.7883 (p) cc_final: 0.7581 (m) REVERT: A 914 ASN cc_start: 0.8360 (p0) cc_final: 0.7977 (p0) REVERT: A 919 ASN cc_start: 0.8792 (m110) cc_final: 0.8422 (m110) REVERT: A 921 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8407 (tptt) REVERT: A 926 GLN cc_start: 0.8469 (mt0) cc_final: 0.8193 (mt0) REVERT: A 933 LYS cc_start: 0.9075 (mttm) cc_final: 0.8324 (mmmm) REVERT: A 949 GLN cc_start: 0.8358 (pp30) cc_final: 0.8088 (pp30) REVERT: A 957 GLN cc_start: 0.8857 (tt0) cc_final: 0.8431 (tm-30) REVERT: A 964 LYS cc_start: 0.8682 (mttt) cc_final: 0.8434 (tptm) REVERT: A 977 LEU cc_start: 0.8803 (tp) cc_final: 0.8424 (pt) REVERT: A 990 GLU cc_start: 0.8052 (tt0) cc_final: 0.7793 (tt0) REVERT: A 991 VAL cc_start: 0.8662 (p) cc_final: 0.8233 (t) REVERT: A 993 ILE cc_start: 0.8863 (mt) cc_final: 0.8384 (tp) REVERT: A 995 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8337 (tpp80) REVERT: A 1012 LEU cc_start: 0.8694 (pp) cc_final: 0.8315 (mt) REVERT: A 1017 GLU cc_start: 0.8071 (tt0) cc_final: 0.7615 (tt0) REVERT: A 1018 ILE cc_start: 0.8478 (mm) cc_final: 0.8192 (mm) REVERT: A 1023 ASN cc_start: 0.8224 (t0) cc_final: 0.7872 (t0) REVERT: A 1028 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8048 (mtpp) REVERT: A 1034 LEU cc_start: 0.8458 (mm) cc_final: 0.7868 (mp) REVERT: A 1045 LYS cc_start: 0.8840 (mppt) cc_final: 0.8497 (mmtm) REVERT: A 1062 PHE cc_start: 0.7169 (m-80) cc_final: 0.6725 (m-80) REVERT: A 1064 HIS cc_start: 0.7052 (m170) cc_final: 0.6801 (m170) REVERT: A 1077 THR cc_start: 0.8209 (t) cc_final: 0.7972 (t) REVERT: A 1088 HIS cc_start: 0.7423 (m-70) cc_final: 0.7120 (m-70) REVERT: A 1101 HIS cc_start: 0.8053 (m90) cc_final: 0.7765 (m170) REVERT: A 1102 TRP cc_start: 0.7932 (m100) cc_final: 0.7473 (m100) REVERT: A 1109 PHE cc_start: 0.8022 (t80) cc_final: 0.7685 (t80) REVERT: B 44 ARG cc_start: 0.8063 (mtt90) cc_final: 0.7846 (mtt90) REVERT: B 53 ASP cc_start: 0.7615 (t0) cc_final: 0.7003 (t0) REVERT: B 54 LEU cc_start: 0.8234 (mp) cc_final: 0.7456 (tt) REVERT: B 58 PHE cc_start: 0.7604 (m-80) cc_final: 0.7197 (m-80) REVERT: B 65 PHE cc_start: 0.8829 (m-80) cc_final: 0.8214 (m-80) REVERT: B 92 PHE cc_start: 0.7444 (t80) cc_final: 0.7235 (t80) REVERT: B 99 ASN cc_start: 0.8501 (t0) cc_final: 0.7916 (t0) REVERT: B 187 LYS cc_start: 0.8669 (pttm) cc_final: 0.8466 (pttm) REVERT: B 206 LYS cc_start: 0.7141 (tptp) cc_final: 0.6497 (ptpt) REVERT: B 207 HIS cc_start: 0.8656 (m-70) cc_final: 0.7537 (m-70) REVERT: B 277 LEU cc_start: 0.7635 (mm) cc_final: 0.7363 (mm) REVERT: B 285 ILE cc_start: 0.8234 (mt) cc_final: 0.8004 (mt) REVERT: B 293 LEU cc_start: 0.8613 (tt) cc_final: 0.8316 (mt) REVERT: B 300 LYS cc_start: 0.8834 (mttt) cc_final: 0.8295 (mttm) REVERT: B 331 ASN cc_start: 0.7815 (t0) cc_final: 0.7355 (m-40) REVERT: B 354 ASN cc_start: 0.8881 (t0) cc_final: 0.8099 (p0) REVERT: B 395 VAL cc_start: 0.8083 (t) cc_final: 0.7733 (m) REVERT: B 409 GLN cc_start: 0.8968 (mt0) cc_final: 0.8242 (tt0) REVERT: B 418 ILE cc_start: 0.8721 (mp) cc_final: 0.8443 (mp) REVERT: B 436 TRP cc_start: 0.8048 (p-90) cc_final: 0.7746 (p-90) REVERT: B 439 ASN cc_start: 0.8360 (p0) cc_final: 0.8117 (t0) REVERT: B 509 ARG cc_start: 0.6492 (mmt180) cc_final: 0.5693 (mmt180) REVERT: B 577 ARG cc_start: 0.7778 (ttt180) cc_final: 0.7303 (ttt180) REVERT: B 582 LEU cc_start: 0.8941 (mt) cc_final: 0.8276 (mt) REVERT: B 583 GLU cc_start: 0.8694 (mp0) cc_final: 0.8331 (mp0) REVERT: B 585 LEU cc_start: 0.8942 (mm) cc_final: 0.8226 (tt) REVERT: B 722 VAL cc_start: 0.8082 (t) cc_final: 0.7823 (t) REVERT: B 753 LEU cc_start: 0.8329 (mm) cc_final: 0.7788 (tt) REVERT: B 758 SER cc_start: 0.8297 (t) cc_final: 0.7970 (m) REVERT: B 759 PHE cc_start: 0.7632 (m-80) cc_final: 0.7239 (m-80) REVERT: B 763 LEU cc_start: 0.8267 (mm) cc_final: 0.7868 (mm) REVERT: B 776 LYS cc_start: 0.8509 (tmtt) cc_final: 0.8090 (tmtt) REVERT: B 778 THR cc_start: 0.8751 (m) cc_final: 0.8367 (p) REVERT: B 779 GLN cc_start: 0.8313 (tp40) cc_final: 0.7673 (tm-30) REVERT: B 780 GLU cc_start: 0.7418 (mm-30) cc_final: 0.6741 (tp30) REVERT: B 786 LYS cc_start: 0.8090 (mppt) cc_final: 0.7739 (mppt) REVERT: B 805 ILE cc_start: 0.8472 (mt) cc_final: 0.8138 (tp) REVERT: B 811 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8473 (mmmt) REVERT: B 819 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7173 (mt-10) REVERT: B 864 LEU cc_start: 0.8428 (tp) cc_final: 0.8168 (tp) REVERT: B 902 MET cc_start: 0.7352 (mmp) cc_final: 0.6965 (tpp) REVERT: B 909 ILE cc_start: 0.7703 (pt) cc_final: 0.7343 (mm) REVERT: B 917 TYR cc_start: 0.7686 (m-10) cc_final: 0.7059 (m-10) REVERT: B 926 GLN cc_start: 0.8144 (mt0) cc_final: 0.7603 (tp40) REVERT: B 934 ILE cc_start: 0.8164 (mm) cc_final: 0.7936 (mm) REVERT: B 935 GLN cc_start: 0.8767 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 954 GLN cc_start: 0.8140 (pp30) cc_final: 0.7802 (pp30) REVERT: B 955 ASN cc_start: 0.8907 (m110) cc_final: 0.7957 (m110) REVERT: B 957 GLN cc_start: 0.8914 (tt0) cc_final: 0.8150 (tp40) REVERT: B 964 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8479 (mmtm) REVERT: B 965 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7867 (tp-100) REVERT: B 970 PHE cc_start: 0.6666 (m-10) cc_final: 0.6207 (m-10) REVERT: B 991 VAL cc_start: 0.8923 (m) cc_final: 0.8635 (t) REVERT: B 1004 LEU cc_start: 0.8613 (mt) cc_final: 0.8378 (mt) REVERT: B 1031 GLU cc_start: 0.6572 (tt0) cc_final: 0.6173 (tt0) REVERT: B 1033 VAL cc_start: 0.7495 (t) cc_final: 0.7097 (t) REVERT: B 1038 LYS cc_start: 0.8678 (tppt) cc_final: 0.8397 (tppt) REVERT: B 1073 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7227 (mmtm) REVERT: B 1109 PHE cc_start: 0.7626 (t80) cc_final: 0.7400 (t80) REVERT: B 1110 TYR cc_start: 0.7965 (t80) cc_final: 0.7724 (t80) REVERT: C 47 VAL cc_start: 0.8832 (m) cc_final: 0.8556 (t) REVERT: C 64 TRP cc_start: 0.7653 (t-100) cc_final: 0.7347 (t-100) REVERT: C 65 PHE cc_start: 0.8756 (m-80) cc_final: 0.7769 (m-80) REVERT: C 99 ASN cc_start: 0.8401 (m-40) cc_final: 0.8182 (m-40) REVERT: C 104 TRP cc_start: 0.6281 (m-90) cc_final: 0.5323 (m-90) REVERT: C 238 PHE cc_start: 0.8482 (p90) cc_final: 0.8280 (p90) REVERT: C 265 TYR cc_start: 0.7367 (p90) cc_final: 0.7074 (p90) REVERT: C 267 VAL cc_start: 0.7290 (t) cc_final: 0.6205 (t) REVERT: C 297 SER cc_start: 0.8066 (m) cc_final: 0.7851 (m) REVERT: C 340 GLU cc_start: 0.9342 (tm-30) cc_final: 0.9128 (tm-30) REVERT: C 364 ASP cc_start: 0.7927 (p0) cc_final: 0.7726 (p0) REVERT: C 370 ASN cc_start: 0.8946 (m-40) cc_final: 0.8423 (p0) REVERT: C 377 PHE cc_start: 0.8057 (t80) cc_final: 0.7843 (t80) REVERT: C 378 LYS cc_start: 0.7702 (tptp) cc_final: 0.7262 (tptp) REVERT: C 440 ASN cc_start: 0.8468 (m-40) cc_final: 0.8048 (p0) REVERT: C 535 LYS cc_start: 0.8589 (mttt) cc_final: 0.7975 (ttmm) REVERT: C 554 GLU cc_start: 0.8522 (tt0) cc_final: 0.8297 (tt0) REVERT: C 557 LYS cc_start: 0.9290 (mttt) cc_final: 0.8870 (mmmt) REVERT: C 563 GLN cc_start: 0.8237 (mt0) cc_final: 0.7742 (tm-30) REVERT: C 577 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7286 (ttm110) REVERT: C 581 THR cc_start: 0.8378 (m) cc_final: 0.8015 (m) REVERT: C 583 GLU cc_start: 0.8747 (mp0) cc_final: 0.8412 (mp0) REVERT: C 759 PHE cc_start: 0.7656 (m-80) cc_final: 0.7368 (m-80) REVERT: C 763 LEU cc_start: 0.8672 (mt) cc_final: 0.8415 (mt) REVERT: C 777 ASN cc_start: 0.8527 (m110) cc_final: 0.8310 (m110) REVERT: C 790 LYS cc_start: 0.8902 (mptt) cc_final: 0.8452 (mmtm) REVERT: C 796 ASP cc_start: 0.8580 (m-30) cc_final: 0.7925 (t0) REVERT: C 808 ASP cc_start: 0.8275 (t70) cc_final: 0.8015 (t0) REVERT: C 894 LEU cc_start: 0.8663 (mt) cc_final: 0.8396 (mm) REVERT: C 921 LYS cc_start: 0.8713 (mmpt) cc_final: 0.8424 (mmtp) REVERT: C 925 ASN cc_start: 0.8657 (m110) cc_final: 0.8400 (m110) REVERT: C 926 GLN cc_start: 0.8510 (mt0) cc_final: 0.8160 (mt0) REVERT: C 936 ASP cc_start: 0.8523 (t0) cc_final: 0.8318 (t0) REVERT: C 953 ASN cc_start: 0.8486 (m110) cc_final: 0.8129 (m110) REVERT: C 964 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8329 (mttp) REVERT: C 965 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8244 (mm-40) REVERT: C 992 GLN cc_start: 0.8330 (pp30) cc_final: 0.7990 (pp30) REVERT: C 1005 GLN cc_start: 0.7817 (tp40) cc_final: 0.7259 (tp40) REVERT: C 1012 LEU cc_start: 0.9004 (mt) cc_final: 0.8633 (mm) REVERT: C 1014 ARG cc_start: 0.7846 (mtt90) cc_final: 0.7388 (ttm-80) REVERT: C 1081 ILE cc_start: 0.8023 (mt) cc_final: 0.7695 (mm) REVERT: C 1088 HIS cc_start: 0.6981 (m-70) cc_final: 0.6455 (m-70) outliers start: 1 outliers final: 0 residues processed: 717 average time/residue: 0.4060 time to fit residues: 449.9825 Evaluate side-chains 670 residues out of total 2826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 203 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 236 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 256 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 263 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.158047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.119564 restraints weight = 55451.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.124335 restraints weight = 34739.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.127784 restraints weight = 24257.800| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.7479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26536 Z= 0.214 Angle : 0.704 15.325 36139 Z= 0.352 Chirality : 0.050 0.606 4208 Planarity : 0.005 0.146 4627 Dihedral : 8.960 88.262 4420 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3207 helix: 0.62 (0.20), residues: 676 sheet: -0.28 (0.20), residues: 652 loop : -1.34 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C1102 HIS 0.015 0.001 HIS A1048 PHE 0.019 0.002 PHE B 157 TYR 0.033 0.002 TYR A 91 ARG 0.022 0.001 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8107.81 seconds wall clock time: 148 minutes 47.63 seconds (8927.63 seconds total)