Starting phenix.real_space_refine on Wed Feb 21 14:11:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a99_15273/02_2024/8a99_15273_updated.pdb" } resolution = 2.5 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= 0.004 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19619 2.51 5 N 5070 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30897 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8292 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8289 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8238 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 52, 'TRANS': 1003} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "P" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 943 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 1, 'RTV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 14, 'RTV': 1} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 14, 'RTV': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 15.53, per 1000 atoms: 0.50 Number of scatterers: 30897 At special positions: 0 Unit cell: (159.58, 167.66, 204.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 6073 8.00 N 5070 7.00 C 19619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 89 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " RTV G 1 " - " NAG G 2 " " RTV H 1 " - " NAG H 2 " " RTV I 1 " - " NAG I 2 " " RTV J 1 " - " NAG J 2 " " RTV K 1 " - " NAG K 2 " " RTV L 1 " - " NAG L 2 " " RTV M 1 " - " NAG M 2 " " RTV N 1 " - " NAG N 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1098 " " NAG A1309 " - " ASN A1134 " " NAG A1310 " - " ASN A 149 " " NAG A1311 " - " ASN A 616 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 801 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 149 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 603 " " NAG B1315 " - " ASN B 801 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 234 " " NAG C1316 " - " ASN C 801 " Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 5.6 seconds 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 62 sheets defined 17.5% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.02 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 756 Processing helix chain 'A' and resid 759 through 782 Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 888 through 890 No H-bonds generated for 'chain 'A' and resid 888 through 890' Processing helix chain 'A' and resid 899 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 946 through 967 removed outlier: 3.979A 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 1032 Processing helix chain 'A' and resid 1142 through 1145 No H-bonds generated for 'chain 'A' and resid 1142 through 1145' Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.611A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 738 through 743 removed outlier: 4.311A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 759 through 782 Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 908 Processing helix chain 'B' and resid 913 through 917 Processing helix chain 'B' and resid 920 through 939 Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.733A 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 1032 Processing helix chain 'B' and resid 1142 through 1145 No H-bonds generated for 'chain 'B' and resid 1142 through 1145' Processing helix chain 'C' and resid 295 through 302 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.076A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 738 through 742 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.984A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 782 Processing helix chain 'C' and resid 817 through 824 Processing helix chain 'C' and resid 867 through 884 Processing helix chain 'C' and resid 898 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 940 Processing helix chain 'C' and resid 946 through 966 Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.201A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1145 No H-bonds generated for 'chain 'C' and resid 1142 through 1145' Processing helix chain 'R' and resid 28 through 31 No H-bonds generated for 'chain 'R' and resid 28 through 31' Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'P' and resid 68 through 71 No H-bonds generated for 'chain 'P' and resid 68 through 71' Processing helix chain 'T' and resid 28 through 31 No H-bonds generated for 'chain 'T' and resid 28 through 31' Processing helix chain 'T' and resid 88 through 90 No H-bonds generated for 'chain 'T' and resid 88 through 90' Processing helix chain 'Q' and resid 30 through 32 No H-bonds generated for 'chain 'Q' and resid 30 through 32' Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 9.316A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.883A 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 50 removed outlier: 3.789A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.526A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 104 through 107 Processing sheet with id= E, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.589A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 243 through 246 removed outlier: 7.224A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 325 through 328 removed outlier: 8.167A pdb=" N ILE A 326 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASN A 540 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ARG A 328 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASN A 542 " --> pdb=" O ARG A 328 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.522A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 642 through 645 removed outlier: 4.111A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 693 through 696 removed outlier: 6.570A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= M, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.656A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id= P, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id= Q, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.523A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY B 89 " --> pdb=" O LEU B 270 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 49 through 55 Processing sheet with id= S, first strand: chain 'B' and resid 116 through 121 Processing sheet with id= T, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.602A pdb=" N ARG B 246 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY B 142 " --> pdb=" O GLU B 156 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU B 156 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.986A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG B 328 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASN B 542 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.715A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (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 551 through 554 removed outlier: 3.777A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.752A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 693 through 696 removed outlier: 6.618A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= AB, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.751A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.383A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 1081 through 1083 Processing sheet with id= AE, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= AF, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.537A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.578A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 168 through 172 removed outlier: 6.288A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 141 through 144 removed outlier: 3.523A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AL, first strand: chain 'C' and resid 538 through 540 removed outlier: 3.606A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 642 through 645 removed outlier: 3.920A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 693 through 696 removed outlier: 6.627A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 711 through 715 Processing sheet with id= AP, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.794A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id= AS, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id= AT, first strand: chain 'C' and resid 565 through 567 removed outlier: 3.639A pdb=" N GLY C 566 " --> pdb=" O ALA C 575 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'R' and resid 9 through 11 removed outlier: 6.644A pdb=" N LEU R 118 " --> pdb=" O GLU R 10 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'R' and resid 18 through 23 removed outlier: 3.540A pdb=" N VAL R 18 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'R' and resid 95 through 99 removed outlier: 3.566A pdb=" N GLY R 49 " --> pdb=" O TRP R 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN R 59 " --> pdb=" O ARG R 50 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'O' and resid 4 through 6 Processing sheet with id= AY, first strand: chain 'O' and resid 86 through 91 removed outlier: 3.619A pdb=" N VAL O 86 " --> pdb=" O GLN O 39 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLN O 38 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU O 47 " --> pdb=" O GLN O 38 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'S' and resid 9 through 11 removed outlier: 7.320A pdb=" N LEU S 118 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL S 18 " --> pdb=" O LEU S 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET S 81 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'S' and resid 95 through 99 removed outlier: 3.635A pdb=" N GLY S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'P' and resid 4 through 6 Processing sheet with id= BD, first strand: chain 'P' and resid 37 through 39 Processing sheet with id= BE, first strand: chain 'P' and resid 63 through 66 removed outlier: 4.204A pdb=" N THR P 73 " --> pdb=" O SER P 66 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'T' and resid 18 through 23 removed outlier: 3.573A pdb=" N VAL T 18 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET T 81 " --> pdb=" O VAL T 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR T 78 " --> pdb=" O ASP T 73 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'T' and resid 95 through 98 removed outlier: 3.546A pdb=" N ASN T 59 " --> pdb=" O ARG T 50 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'T' and resid 92 through 94 Processing sheet with id= BI, first strand: chain 'Q' and resid 4 through 6 Processing sheet with id= BJ, first strand: chain 'Q' and resid 86 through 91 removed outlier: 3.534A pdb=" N VAL Q 86 " --> pdb=" O GLN Q 39 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE Q 49 " --> pdb=" O TRP Q 36 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N GLN Q 38 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU Q 47 " --> pdb=" O GLN Q 38 " (cutoff:3.500A) 970 hydrogen bonds defined for protein. 2691 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: 14.50 Time building geometry restraints manager: 14.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6307 1.33 - 1.46: 9026 1.46 - 1.58: 16081 1.58 - 1.71: 6 1.71 - 1.84: 174 Bond restraints: 31594 Sorted by residual: bond pdb=" CG1 ILE C 402 " pdb=" CD1 ILE C 402 " ideal model delta sigma weight residual 1.513 1.293 0.220 3.90e-02 6.57e+02 3.18e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.495 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CB THR B 393 " pdb=" CG2 THR B 393 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.56e+01 bond pdb=" CA THR Q 10 " pdb=" CB THR Q 10 " ideal model delta sigma weight residual 1.531 1.579 -0.049 1.34e-02 5.57e+03 1.32e+01 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.472 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 31589 not shown) Histogram of bond angle deviations from ideal: 97.07 - 105.16: 617 105.16 - 113.26: 16788 113.26 - 121.35: 16802 121.35 - 129.45: 8599 129.45 - 137.54: 176 Bond angle restraints: 42982 Sorted by residual: angle pdb=" N PRO A 899 " pdb=" CA PRO A 899 " pdb=" CB PRO A 899 " ideal model delta sigma weight residual 103.25 110.88 -7.63 1.05e+00 9.07e-01 5.28e+01 angle pdb=" C LEU C 518 " pdb=" N HIS C 519 " pdb=" CA HIS C 519 " ideal model delta sigma weight residual 121.54 134.83 -13.29 1.91e+00 2.74e-01 4.84e+01 angle pdb=" N PRO C 899 " pdb=" CA PRO C 899 " pdb=" CB PRO C 899 " ideal model delta sigma weight residual 103.25 110.37 -7.12 1.05e+00 9.07e-01 4.59e+01 angle pdb=" N ARG B 78 " pdb=" CA ARG B 78 " pdb=" C ARG B 78 " ideal model delta sigma weight residual 111.39 120.05 -8.66 1.38e+00 5.25e-01 3.94e+01 angle pdb=" CA LEU C 492 " pdb=" CB LEU C 492 " pdb=" CG LEU C 492 " ideal model delta sigma weight residual 116.30 137.54 -21.24 3.50e+00 8.16e-02 3.68e+01 ... (remaining 42977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 18818 33.26 - 66.52: 511 66.52 - 99.77: 146 99.77 - 133.03: 37 133.03 - 166.29: 4 Dihedral angle restraints: 19516 sinusoidal: 8306 harmonic: 11210 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 168.87 -75.87 1 1.00e+01 1.00e-02 7.26e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 154.04 -61.04 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -25.45 -60.55 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 19513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.002: 4978 1.002 - 2.004: 1 2.004 - 3.006: 0 3.006 - 4.008: 0 4.008 - 5.010: 11 Chirality restraints: 4990 Sorted by residual: chirality pdb=" C2 RTV C1311 " pdb=" C1 RTV C1311 " pdb=" C3 RTV C1311 " pdb=" N2 RTV C1311 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C2 RTV B1314 " pdb=" C1 RTV B1314 " pdb=" C3 RTV B1314 " pdb=" N2 RTV B1314 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C2 RTV I 1 " pdb=" C1 RTV I 1 " pdb=" C3 RTV I 1 " pdb=" N2 RTV I 1 " both_signs ideal model delta sigma weight residual False 2.50 -2.51 5.01 2.00e-01 2.50e+01 6.27e+02 ... (remaining 4987 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 508 " 0.065 2.00e-02 2.50e+03 4.51e-02 4.07e+01 pdb=" CG TYR C 508 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 TYR C 508 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR C 508 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 508 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 508 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 508 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 508 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 138 " -0.083 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO A 139 " 0.223 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 342 " 0.035 2.00e-02 2.50e+03 3.34e-02 1.95e+01 pdb=" CG PHE A 342 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 342 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 342 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 342 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 342 " 0.025 2.00e-02 2.50e+03 pdb=" CZ PHE A 342 " -0.003 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2691 2.75 - 3.29: 29508 3.29 - 3.83: 53079 3.83 - 4.36: 61739 4.36 - 4.90: 106243 Nonbonded interactions: 253260 Sorted by model distance: nonbonded pdb=" O TYR P 50 " pdb=" OG SER P 54 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR R 120 " pdb=" O SER R 122 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR S 120 " pdb=" O SER S 122 " model vdw 2.225 2.440 nonbonded pdb=" O PHE B 464 " pdb=" O6 NAG C1315 " model vdw 2.243 2.440 nonbonded pdb=" OG1 THR T 120 " pdb=" O SER T 122 " model vdw 2.245 2.440 ... (remaining 253255 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 14 through 531 or (resid 532 through 533 and (name N or na \ me CA or name C or name O or name CB )) or resid 534 through 577 or resid 584 th \ rough 1146 or resid 1301 through 1310 or resid 1313)) selection = (chain 'B' and (resid 14 through 532 or (resid 533 and (name N or name CA or nam \ e C or name O or name CB )) or resid 534 through 577 or resid 584 through 1146 o \ r resid 1301 through 1310 or resid 1313)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1310 or resid 1313)) \ } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.000 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: 28.730 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 86.690 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.370 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.220 31594 Z= 0.466 Angle : 1.228 21.241 42982 Z= 0.655 Chirality : 0.248 5.010 4990 Planarity : 0.008 0.129 5489 Dihedral : 17.405 166.291 12205 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.21 % Allowed : 0.87 % Favored : 98.92 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3814 helix: 2.14 (0.20), residues: 688 sheet: 0.48 (0.18), residues: 848 loop : -1.06 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP C 886 HIS 0.014 0.002 HIS C 245 PHE 0.073 0.004 PHE A 342 TYR 0.108 0.004 TYR C 508 ARG 0.054 0.001 ARG T 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 521 time to evaluate : 3.702 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: B 866 THR cc_start: 0.7610 (p) cc_final: 0.7282 (t) REVERT: R 102 TYR cc_start: 0.4275 (m-80) cc_final: 0.3954 (m-80) REVERT: S 69 THR cc_start: 0.9106 (m) cc_final: 0.8876 (p) REVERT: P 48 LEU cc_start: 0.8224 (mp) cc_final: 0.8023 (pp) REVERT: P 49 ILE cc_start: 0.7517 (pt) cc_final: 0.7122 (pt) REVERT: P 72 PHE cc_start: 0.8818 (p90) cc_final: 0.8448 (p90) outliers start: 7 outliers final: 4 residues processed: 526 average time/residue: 1.1963 time to fit residues: 763.4925 Evaluate side-chains 286 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 282 time to evaluate : 3.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain O residue 92 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 323 optimal weight: 9.9990 chunk 290 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 223 optimal weight: 0.9980 chunk 347 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 450 ASN B 949 GLN B 954 GLN B1005 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN C 655 HIS ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN C 965 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN T 6 GLN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31594 Z= 0.298 Angle : 0.777 13.443 42982 Z= 0.385 Chirality : 0.057 0.576 4990 Planarity : 0.005 0.073 5489 Dihedral : 12.573 149.600 5431 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 2.38 % Allowed : 12.61 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.23 (0.13), residues: 3814 helix: 1.76 (0.20), residues: 679 sheet: 0.32 (0.17), residues: 892 loop : -0.98 (0.12), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 152 HIS 0.010 0.001 HIS C 519 PHE 0.038 0.002 PHE A 515 TYR 0.026 0.002 TYR C 170 ARG 0.013 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 295 time to evaluate : 3.323 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: B 795 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.5789 (mtpp) REVERT: S 20 VAL cc_start: 0.7509 (t) cc_final: 0.7258 (t) REVERT: S 45 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.6037 (mt) REVERT: S 82 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7982 (tm-30) REVERT: S 83 LEU cc_start: 0.9179 (mm) cc_final: 0.8448 (pp) REVERT: P 21 LEU cc_start: 0.6385 (mp) cc_final: 0.6100 (mp) REVERT: P 72 PHE cc_start: 0.8715 (p90) cc_final: 0.8386 (p90) REVERT: T 36 TRP cc_start: 0.7243 (t-100) cc_final: 0.6863 (t-100) outliers start: 79 outliers final: 35 residues processed: 343 average time/residue: 1.1548 time to fit residues: 489.2451 Evaluate side-chains 273 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1058 HIS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 964 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 32 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain P residue 50 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 193 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 289 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 348 optimal weight: 10.0000 chunk 376 optimal weight: 30.0000 chunk 310 optimal weight: 0.0980 chunk 345 optimal weight: 0.3980 chunk 118 optimal weight: 3.9990 chunk 279 optimal weight: 0.0270 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** S 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 ASN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31594 Z= 0.198 Angle : 0.652 11.025 42982 Z= 0.326 Chirality : 0.050 0.537 4990 Planarity : 0.005 0.088 5489 Dihedral : 10.733 143.362 5426 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 2.95 % Allowed : 14.95 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.25 (0.13), residues: 3814 helix: 1.90 (0.20), residues: 673 sheet: 0.24 (0.17), residues: 896 loop : -1.02 (0.12), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 152 HIS 0.008 0.001 HIS B1058 PHE 0.027 0.002 PHE A 565 TYR 0.020 0.002 TYR A 265 ARG 0.010 0.001 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 245 time to evaluate : 3.861 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: A 780 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: A 1017 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: S 20 VAL cc_start: 0.7248 (t) cc_final: 0.6727 (t) REVERT: S 45 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6059 (tp) REVERT: S 82 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7648 (tm-30) REVERT: S 83 LEU cc_start: 0.8902 (mm) cc_final: 0.8268 (pp) REVERT: S 110 LEU cc_start: 0.7238 (mm) cc_final: 0.7019 (mm) REVERT: P 72 PHE cc_start: 0.8620 (p90) cc_final: 0.8304 (p90) outliers start: 98 outliers final: 36 residues processed: 318 average time/residue: 1.0301 time to fit residues: 411.5836 Evaluate side-chains 257 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 6 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 344 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 349 optimal weight: 4.9990 chunk 370 optimal weight: 20.0000 chunk 182 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 14 GLN B 955 ASN B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 779 GLN C1088 HIS S 6 GLN ** P 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 31594 Z= 0.422 Angle : 0.795 14.791 42982 Z= 0.404 Chirality : 0.056 0.485 4990 Planarity : 0.005 0.074 5489 Dihedral : 9.498 135.285 5421 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 3.94 % Allowed : 16.16 % Favored : 79.90 % 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: -0.75 (0.13), residues: 3814 helix: 1.08 (0.19), residues: 675 sheet: 0.01 (0.17), residues: 882 loop : -1.25 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP S 47 HIS 0.009 0.002 HIS A1058 PHE 0.031 0.003 PHE S 29 TYR 0.031 0.002 TYR B1067 ARG 0.011 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 248 time to evaluate : 3.650 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: A 275 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.5996 (t80) REVERT: A 780 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6606 (tm-30) REVERT: B 59 PHE cc_start: 0.6365 (m-10) cc_final: 0.6149 (m-80) REVERT: B 79 PHE cc_start: 0.4465 (OUTLIER) cc_final: 0.3601 (m-80) REVERT: C 281 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5165 (pp20) REVERT: C 878 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8159 (mm) REVERT: R 48 MET cc_start: 0.7352 (pmm) cc_final: 0.6761 (pmm) REVERT: R 54 MET cc_start: 0.3056 (mpp) cc_final: 0.2796 (pmm) REVERT: S 83 LEU cc_start: 0.8716 (mm) cc_final: 0.8170 (pp) REVERT: P 72 PHE cc_start: 0.8636 (p90) cc_final: 0.8306 (p90) REVERT: T 48 MET cc_start: 0.6379 (mmp) cc_final: 0.6122 (mtp) outliers start: 131 outliers final: 58 residues processed: 348 average time/residue: 0.9924 time to fit residues: 437.4611 Evaluate side-chains 276 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 213 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain P residue 98 THR Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 6 GLN Chi-restraints excluded: chain Q residue 11 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 308 optimal weight: 0.9990 chunk 210 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 315 optimal weight: 0.6980 chunk 255 optimal weight: 0.0170 chunk 0 optimal weight: 20.0000 chunk 189 optimal weight: 0.2980 chunk 332 optimal weight: 50.0000 chunk 93 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 804 GLN A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31594 Z= 0.207 Angle : 0.645 12.005 42982 Z= 0.324 Chirality : 0.048 0.457 4990 Planarity : 0.004 0.063 5489 Dihedral : 8.538 123.297 5421 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 3.01 % Allowed : 18.74 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.57 (0.13), residues: 3814 helix: 1.63 (0.20), residues: 657 sheet: -0.03 (0.17), residues: 877 loop : -1.17 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 436 HIS 0.005 0.001 HIS C 519 PHE 0.037 0.002 PHE S 29 TYR 0.025 0.001 TYR B 473 ARG 0.008 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 236 time to evaluate : 3.204 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: A 275 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.6007 (t80) REVERT: A 780 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: B 79 PHE cc_start: 0.4237 (OUTLIER) cc_final: 0.3529 (m-80) REVERT: B 795 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.5987 (mtpp) REVERT: C 693 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8041 (pp) REVERT: C 878 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8055 (mm) REVERT: S 83 LEU cc_start: 0.8675 (mm) cc_final: 0.7962 (pp) REVERT: S 110 LEU cc_start: 0.7006 (mm) cc_final: 0.6749 (tp) REVERT: P 72 PHE cc_start: 0.8610 (p90) cc_final: 0.8290 (p90) REVERT: T 6 GLN cc_start: 0.4756 (OUTLIER) cc_final: 0.3116 (mm110) outliers start: 100 outliers final: 45 residues processed: 311 average time/residue: 1.0604 time to fit residues: 412.3877 Evaluate side-chains 256 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 124 optimal weight: 2.9990 chunk 333 optimal weight: 40.0000 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 370 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 171 optimal weight: 0.0980 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 31594 Z= 0.342 Angle : 0.710 18.809 42982 Z= 0.358 Chirality : 0.051 0.441 4990 Planarity : 0.005 0.072 5489 Dihedral : 8.137 111.346 5421 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.85 % Favored : 95.10 % Rotamer: Outliers : 3.73 % Allowed : 18.95 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.75 (0.13), residues: 3814 helix: 1.30 (0.20), residues: 675 sheet: -0.12 (0.17), residues: 839 loop : -1.24 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 436 HIS 0.007 0.001 HIS A1058 PHE 0.033 0.002 PHE A 817 TYR 0.029 0.002 TYR B1067 ARG 0.011 0.001 ARG S 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 210 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6527 (tm-30) REVERT: B 79 PHE cc_start: 0.4446 (OUTLIER) cc_final: 0.3618 (m-80) REVERT: B 795 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6260 (mtpp) REVERT: C 693 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8113 (pt) REVERT: C 878 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8139 (mm) REVERT: S 37 VAL cc_start: 0.8733 (m) cc_final: 0.8398 (p) REVERT: S 82 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7763 (tp30) REVERT: S 83 LEU cc_start: 0.8503 (mm) cc_final: 0.7928 (pp) REVERT: T 36 TRP cc_start: 0.7339 (OUTLIER) cc_final: 0.7115 (t-100) outliers start: 124 outliers final: 62 residues processed: 311 average time/residue: 1.0046 time to fit residues: 396.8725 Evaluate side-chains 269 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 201 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain O residue 93 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 6 GLN Chi-restraints excluded: chain T residue 36 TRP Chi-restraints excluded: chain Q residue 10 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 357 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 270 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 311 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 369 optimal weight: 6.9990 chunk 231 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS C 122 ASN C 196 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31594 Z= 0.325 Angle : 0.718 14.241 42982 Z= 0.360 Chirality : 0.051 0.472 4990 Planarity : 0.005 0.073 5489 Dihedral : 7.803 96.861 5421 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 3.76 % Allowed : 19.34 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.82 (0.13), residues: 3814 helix: 1.26 (0.20), residues: 671 sheet: -0.17 (0.17), residues: 851 loop : -1.29 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 47 HIS 0.005 0.001 HIS C1048 PHE 0.047 0.002 PHE A 565 TYR 0.026 0.002 TYR B1067 ARG 0.009 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 203 time to evaluate : 3.145 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: A 780 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: B 79 PHE cc_start: 0.4689 (OUTLIER) cc_final: 0.3375 (m-80) REVERT: B 795 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7000 (mtpp) REVERT: B 900 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6794 (mtp) REVERT: C 693 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8141 (pt) REVERT: C 878 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8123 (mm) REVERT: R 48 MET cc_start: 0.6520 (pmm) cc_final: 0.6265 (pmm) REVERT: S 37 VAL cc_start: 0.8670 (m) cc_final: 0.8362 (p) REVERT: S 83 LEU cc_start: 0.8445 (mm) cc_final: 0.7990 (pp) REVERT: S 110 LEU cc_start: 0.7263 (mm) cc_final: 0.7049 (tp) outliers start: 125 outliers final: 67 residues processed: 300 average time/residue: 0.9730 time to fit residues: 370.1177 Evaluate side-chains 259 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 186 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain T residue 6 GLN Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 228 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 220 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31594 Z= 0.314 Angle : 0.715 18.697 42982 Z= 0.358 Chirality : 0.050 0.410 4990 Planarity : 0.005 0.099 5489 Dihedral : 7.493 81.164 5421 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.76 % Rotamer: Outliers : 3.31 % Allowed : 20.46 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % 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: -0.82 (0.13), residues: 3814 helix: 1.26 (0.20), residues: 669 sheet: -0.11 (0.17), residues: 844 loop : -1.31 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 47 HIS 0.007 0.001 HIS C 519 PHE 0.031 0.002 PHE A 392 TYR 0.026 0.002 TYR B1067 ARG 0.008 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 199 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7240 (ptm) REVERT: A 780 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: B 79 PHE cc_start: 0.4724 (OUTLIER) cc_final: 0.3433 (m-80) REVERT: B 795 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7052 (mtpp) REVERT: B 900 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6810 (mtp) REVERT: C 693 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8149 (pt) REVERT: C 878 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8142 (mm) REVERT: S 70 PHE cc_start: 0.6418 (m-10) cc_final: 0.5985 (m-80) REVERT: S 83 LEU cc_start: 0.8508 (mm) cc_final: 0.8116 (pp) outliers start: 110 outliers final: 64 residues processed: 286 average time/residue: 0.9391 time to fit residues: 342.4047 Evaluate side-chains 258 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 187 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 605 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 335 optimal weight: 0.2980 chunk 353 optimal weight: 30.0000 chunk 322 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 310 optimal weight: 2.9990 chunk 325 optimal weight: 30.0000 chunk 342 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 31594 Z= 0.327 Angle : 0.721 15.783 42982 Z= 0.363 Chirality : 0.051 0.402 4990 Planarity : 0.005 0.090 5489 Dihedral : 7.315 77.102 5421 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 3.07 % Allowed : 20.94 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 3814 helix: 1.21 (0.20), residues: 672 sheet: -0.14 (0.17), residues: 888 loop : -1.34 (0.12), residues: 2254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP R 47 HIS 0.005 0.001 HIS A1058 PHE 0.030 0.002 PHE A 817 TYR 0.027 0.002 TYR B1067 ARG 0.008 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 196 time to evaluate : 3.457 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: A 697 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7245 (ptm) REVERT: A 780 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: B 79 PHE cc_start: 0.4797 (OUTLIER) cc_final: 0.3528 (m-80) REVERT: B 795 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7109 (mtpp) REVERT: B 900 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6808 (mtp) REVERT: C 693 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8173 (pt) REVERT: C 878 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 900 MET cc_start: 0.7821 (mtp) cc_final: 0.7617 (ttm) REVERT: R 48 MET cc_start: 0.6316 (pmm) cc_final: 0.6080 (pmm) REVERT: R 81 MET cc_start: 0.0506 (mpm) cc_final: -0.0959 (mmm) REVERT: S 83 LEU cc_start: 0.9022 (mm) cc_final: 0.8106 (pp) outliers start: 102 outliers final: 70 residues processed: 278 average time/residue: 0.9919 time to fit residues: 352.3376 Evaluate side-chains 259 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 182 time to evaluate : 3.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 30 ASN Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 225 optimal weight: 3.9990 chunk 363 optimal weight: 50.0000 chunk 222 optimal weight: 0.8980 chunk 172 optimal weight: 0.7980 chunk 252 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 351 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 186 optimal weight: 0.0870 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 957 GLN B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31594 Z= 0.241 Angle : 0.690 17.397 42982 Z= 0.342 Chirality : 0.049 0.396 4990 Planarity : 0.005 0.084 5489 Dihedral : 7.000 73.358 5421 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.85 % Favored : 95.12 % Rotamer: Outliers : 2.77 % Allowed : 21.66 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 3814 helix: 1.51 (0.20), residues: 665 sheet: -0.05 (0.17), residues: 883 loop : -1.32 (0.12), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP S 36 HIS 0.006 0.001 HIS C 519 PHE 0.029 0.002 PHE S 64 TYR 0.023 0.001 TYR P 87 ARG 0.008 0.001 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7628 Ramachandran restraints generated. 3814 Oldfield, 0 Emsley, 3814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 193 time to evaluate : 3.545 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: A 780 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: B 795 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7077 (mtpp) REVERT: B 900 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6792 (mtp) REVERT: C 693 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8105 (pp) REVERT: C 878 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8132 (mm) REVERT: P 91 GLN cc_start: 0.7865 (tp40) cc_final: 0.7489 (tp-100) outliers start: 92 outliers final: 70 residues processed: 265 average time/residue: 0.9706 time to fit residues: 329.8150 Evaluate side-chains 255 residues out of total 3339 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 180 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 88 TYR Chi-restraints excluded: chain S residue 30 ASN Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 241 optimal weight: 1.9990 chunk 323 optimal weight: 30.0000 chunk 93 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.190415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.142937 restraints weight = 57523.026| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 4.38 r_work: 0.3732 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 31594 Z= 0.336 Angle : 0.727 17.246 42982 Z= 0.365 Chirality : 0.051 0.396 4990 Planarity : 0.005 0.082 5489 Dihedral : 6.946 69.683 5421 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.71 % Allowed : 21.72 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.53 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3814 helix: 1.25 (0.20), residues: 675 sheet: -0.07 (0.17), residues: 848 loop : -1.32 (0.12), residues: 2291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP R 47 HIS 0.006 0.001 HIS C1048 PHE 0.031 0.002 PHE A 392 TYR 0.046 0.002 TYR A 200 ARG 0.018 0.001 ARG R 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10576.33 seconds wall clock time: 190 minutes 17.68 seconds (11417.68 seconds total)