Starting phenix.real_space_refine on Sun Mar 17 23:18:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwq_23554/03_2024/7lwq_23554.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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 84 5.16 5 C 12268 2.51 5 N 3171 2.21 5 O 3750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19273 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3250 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain breaks: 1 Chain: "C" Number of atoms: 7808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7808 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 10.79, per 1000 atoms: 0.56 Number of scatterers: 19273 At special positions: 0 Unit cell: (127.211, 124.004, 177.454, 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 84 16.00 O 3750 8.00 N 3171 7.00 C 12268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.05 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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 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 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A1098 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C1098 " " NAG D 1 " - " ASN B1134 " Time building additional restraints: 7.48 Conformation dependent library (CDL) restraints added in 3.4 seconds 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 37 sheets defined 31.3% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 5.232A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.028A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.557A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.538A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.900A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.691A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.638A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.720A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.754A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 5.468A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.548A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.680A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.733A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.755A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.662A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.379A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.796A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.294A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.581A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.836A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.156A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.453A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.806A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.605A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.540A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.545A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.775A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.965A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.558A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.396A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.925A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 90 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE A 192 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.472A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 552 " --> pdb=" O LYS C 537 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS C 537 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.746A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.131A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.902A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 5.398A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.009A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.571A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 567 removed outlier: 4.791A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.741A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.573A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.503A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A1068 " --> pdb=" O THR A 719 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.254A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.642A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.769A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.524A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.680A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.063A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.949A pdb=" N THR C 51 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.532A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.713A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AD3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.763A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.640A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.510A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2388 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: 7.74 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4917 1.33 - 1.46: 3773 1.46 - 1.58: 10883 1.58 - 1.70: 0 1.70 - 1.82: 107 Bond restraints: 19680 Sorted by residual: bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG A1312 " pdb=" O5 NAG A1312 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 19675 not shown) Histogram of bond angle deviations from ideal: 97.61 - 105.18: 356 105.18 - 112.75: 9398 112.75 - 120.32: 9607 120.32 - 127.89: 7330 127.89 - 135.45: 77 Bond angle restraints: 26768 Sorted by residual: angle pdb=" CA PHE A 201 " pdb=" CB PHE A 201 " pdb=" CG PHE A 201 " ideal model delta sigma weight residual 113.80 119.33 -5.53 1.00e+00 1.00e+00 3.06e+01 angle pdb=" CB HIS A1064 " pdb=" CG HIS A1064 " pdb=" CD2 HIS A1064 " ideal model delta sigma weight residual 131.20 124.46 6.74 1.30e+00 5.92e-01 2.69e+01 angle pdb=" OE1 GLN C 965 " pdb=" CD GLN C 965 " pdb=" NE2 GLN C 965 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N LEU A 229 " pdb=" CA LEU A 229 " pdb=" C LEU A 229 " ideal model delta sigma weight residual 110.07 116.51 -6.44 1.26e+00 6.30e-01 2.62e+01 angle pdb=" OE1 GLN B1054 " pdb=" CD GLN B1054 " pdb=" NE2 GLN B1054 " ideal model delta sigma weight residual 122.60 117.51 5.09 1.00e+00 1.00e+00 2.59e+01 ... (remaining 26763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11214 17.92 - 35.84: 711 35.84 - 53.77: 123 53.77 - 71.69: 33 71.69 - 89.61: 41 Dihedral angle restraints: 12122 sinusoidal: 5077 harmonic: 7045 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 177.38 -84.38 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CA SER A 221 " pdb=" C SER A 221 " pdb=" N ALA A 222 " pdb=" CA ALA A 222 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA PRO C 807 " pdb=" C PRO C 807 " pdb=" N ASP C 808 " pdb=" CA ASP C 808 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 12119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.278: 3138 0.278 - 0.556: 20 0.556 - 0.835: 0 0.835 - 1.113: 0 1.113 - 1.391: 1 Chirality restraints: 3159 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.84e+01 chirality pdb=" CA ASP C 745 " pdb=" N ASP C 745 " pdb=" C ASP C 745 " pdb=" CB ASP C 745 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 3156 not shown) Planarity restraints: 3455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 282 " 0.139 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN C 282 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN C 282 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 282 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG C1302 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.141 2.00e-02 2.50e+03 1.49e-01 2.77e+02 pdb=" CG ASN C 331 " -0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.227 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 204 " 0.211 2.00e-02 2.50e+03 1.15e-01 2.66e+02 pdb=" CG TYR A 204 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A 204 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 TYR A 204 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR A 204 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 204 " -0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 204 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 204 " 0.167 2.00e-02 2.50e+03 ... (remaining 3452 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 9722 3.00 - 3.47: 19114 3.47 - 3.95: 31871 3.95 - 4.42: 34877 4.42 - 4.90: 58874 Nonbonded interactions: 154458 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.519 2.440 nonbonded pdb=" OG1 THR A 581 " pdb=" OE1 GLU A 583 " model vdw 2.543 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.549 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.557 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.564 2.440 ... (remaining 154453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 1147 or resid 1301 through 1312 \ )) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.910 Check model and map are aligned: 0.320 Set scattering table: 0.200 Process input model: 53.780 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 : 0.013 0.078 19680 Z= 0.860 Angle : 1.771 13.073 26768 Z= 1.185 Chirality : 0.100 1.391 3159 Planarity : 0.014 0.200 3427 Dihedral : 13.593 89.610 7493 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.57 % Favored : 93.05 % Rotamer: Outliers : 1.18 % Allowed : 3.27 % Favored : 95.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.15), residues: 2389 helix: -0.82 (0.17), residues: 653 sheet: -0.13 (0.23), residues: 395 loop : -1.14 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.025 TRP C 104 HIS 0.009 0.003 HIS A 655 PHE 0.126 0.012 PHE A 86 TYR 0.211 0.023 TYR A 204 ARG 0.010 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 258 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5368 (mt) REVERT: A 590 CYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4215 (p) REVERT: B 856 ASN cc_start: 0.7221 (m-40) cc_final: 0.6822 (m-40) REVERT: B 1142 GLN cc_start: 0.9123 (tp40) cc_final: 0.8807 (tp-100) REVERT: C 195 LYS cc_start: 0.6347 (pttt) cc_final: 0.6019 (ptpp) REVERT: C 552 LEU cc_start: 0.9237 (mt) cc_final: 0.8826 (tp) REVERT: C 907 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8721 (t0) REVERT: C 1029 MET cc_start: 0.9255 (tpp) cc_final: 0.8892 (tpp) outliers start: 25 outliers final: 6 residues processed: 280 average time/residue: 0.3271 time to fit residues: 137.5757 Evaluate side-chains 133 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 124 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 189 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 370 ASN A 613 GLN A 779 GLN A 960 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 675 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19680 Z= 0.195 Angle : 0.658 7.969 26768 Z= 0.351 Chirality : 0.048 0.393 3159 Planarity : 0.004 0.045 3427 Dihedral : 7.548 59.268 3205 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.06 % Favored : 96.82 % Rotamer: Outliers : 1.47 % Allowed : 7.53 % Favored : 91.00 % 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: -0.26 (0.16), residues: 2389 helix: 1.23 (0.20), residues: 646 sheet: -0.15 (0.21), residues: 479 loop : -0.91 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 436 HIS 0.004 0.001 HIS A 49 PHE 0.042 0.002 PHE C 823 TYR 0.022 0.002 TYR C 369 ARG 0.004 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 156 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.8352 (p0) cc_final: 0.8128 (p0) REVERT: A 242 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 559 PHE cc_start: -0.0861 (OUTLIER) cc_final: -0.2189 (m-80) REVERT: A 590 CYS cc_start: 0.4797 (OUTLIER) cc_final: 0.4349 (p) REVERT: A 779 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7412 (tp-100) REVERT: A 947 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8355 (mttp) REVERT: B 856 ASN cc_start: 0.7190 (m-40) cc_final: 0.6917 (m-40) REVERT: C 784 GLN cc_start: 0.6951 (mm110) cc_final: 0.6610 (mm110) REVERT: C 907 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8719 (t0) REVERT: C 1029 MET cc_start: 0.9223 (tpp) cc_final: 0.8910 (tpp) REVERT: C 1141 LEU cc_start: 0.9514 (tp) cc_final: 0.9309 (mm) outliers start: 31 outliers final: 11 residues processed: 180 average time/residue: 0.2960 time to fit residues: 84.6975 Evaluate side-chains 126 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 109 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 196 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 784 GLN A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19680 Z= 0.278 Angle : 0.619 6.591 26768 Z= 0.326 Chirality : 0.046 0.347 3159 Planarity : 0.004 0.038 3427 Dihedral : 7.011 58.868 3192 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.99 % Allowed : 9.52 % Favored : 88.49 % 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: -0.22 (0.16), residues: 2389 helix: 1.48 (0.21), residues: 651 sheet: -0.27 (0.21), residues: 483 loop : -0.97 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS A1064 PHE 0.019 0.002 PHE C 823 TYR 0.024 0.002 TYR A 508 ARG 0.004 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8461 (mt) cc_final: 0.8192 (mp) REVERT: A 559 PHE cc_start: -0.0449 (OUTLIER) cc_final: -0.1907 (m-80) REVERT: A 568 ASP cc_start: 0.6305 (t0) cc_final: 0.5896 (m-30) REVERT: A 590 CYS cc_start: 0.4879 (OUTLIER) cc_final: 0.4488 (p) REVERT: A 947 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8271 (mttp) REVERT: A 1019 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7216 (ttp80) REVERT: C 552 LEU cc_start: 0.9096 (mp) cc_final: 0.8301 (tp) REVERT: C 784 GLN cc_start: 0.6843 (mm110) cc_final: 0.6560 (mm110) REVERT: C 907 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8730 (t0) outliers start: 42 outliers final: 24 residues processed: 143 average time/residue: 0.2750 time to fit residues: 65.8316 Evaluate side-chains 123 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 217 optimal weight: 2.9990 chunk 165 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 147 optimal weight: 40.0000 chunk 220 optimal weight: 7.9990 chunk 233 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN A 955 ASN A1005 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19680 Z= 0.176 Angle : 0.544 7.645 26768 Z= 0.285 Chirality : 0.044 0.291 3159 Planarity : 0.004 0.037 3427 Dihedral : 6.476 59.327 3192 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 10.00 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.00 (0.17), residues: 2389 helix: 1.82 (0.21), residues: 653 sheet: -0.20 (0.21), residues: 479 loop : -0.90 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C 207 PHE 0.016 0.001 PHE A 400 TYR 0.022 0.001 TYR A 904 ARG 0.004 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8494 (mt) cc_final: 0.8217 (mp) REVERT: A 559 PHE cc_start: -0.0229 (OUTLIER) cc_final: -0.1789 (m-80) REVERT: A 568 ASP cc_start: 0.6627 (t0) cc_final: 0.6112 (m-30) REVERT: A 590 CYS cc_start: 0.4965 (OUTLIER) cc_final: 0.3021 (p) REVERT: A 947 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8267 (mttp) REVERT: A 1019 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7369 (ttp-110) REVERT: B 990 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6668 (tm-30) REVERT: C 552 LEU cc_start: 0.9096 (mp) cc_final: 0.8300 (tp) REVERT: C 784 GLN cc_start: 0.7028 (mm110) cc_final: 0.6816 (mm110) REVERT: C 907 ASN cc_start: 0.9048 (OUTLIER) cc_final: 0.8704 (t0) outliers start: 44 outliers final: 25 residues processed: 162 average time/residue: 0.2681 time to fit residues: 72.2704 Evaluate side-chains 125 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 194 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 174 optimal weight: 0.0670 chunk 96 optimal weight: 0.7980 chunk 199 optimal weight: 8.9990 chunk 161 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 354 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19680 Z= 0.181 Angle : 0.537 8.284 26768 Z= 0.278 Chirality : 0.044 0.278 3159 Planarity : 0.003 0.038 3427 Dihedral : 6.224 59.221 3192 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 1.71 % Allowed : 10.66 % Favored : 87.64 % 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: 0.04 (0.17), residues: 2389 helix: 1.87 (0.21), residues: 652 sheet: -0.21 (0.22), residues: 467 loop : -0.87 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.003 0.001 HIS A 655 PHE 0.016 0.001 PHE A 400 TYR 0.021 0.001 TYR C1067 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7540 (ptpp) REVERT: A 229 LEU cc_start: 0.7097 (mt) cc_final: 0.6732 (tt) REVERT: A 441 LEU cc_start: 0.8552 (mt) cc_final: 0.8285 (mp) REVERT: A 559 PHE cc_start: -0.0070 (OUTLIER) cc_final: -0.1640 (m-80) REVERT: A 568 ASP cc_start: 0.6784 (t0) cc_final: 0.6189 (m-30) REVERT: A 590 CYS cc_start: 0.3396 (OUTLIER) cc_final: 0.1660 (p) REVERT: A 947 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8038 (mttp) REVERT: B 990 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6715 (tm-30) REVERT: C 907 ASN cc_start: 0.9116 (OUTLIER) cc_final: 0.8714 (t0) outliers start: 36 outliers final: 19 residues processed: 141 average time/residue: 0.2635 time to fit residues: 61.4562 Evaluate side-chains 123 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 78 optimal weight: 4.9990 chunk 210 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19680 Z= 0.192 Angle : 0.528 9.644 26768 Z= 0.273 Chirality : 0.044 0.265 3159 Planarity : 0.003 0.037 3427 Dihedral : 6.067 59.761 3192 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 2.18 % Allowed : 10.75 % Favored : 87.07 % 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: 0.07 (0.17), residues: 2389 helix: 1.94 (0.21), residues: 652 sheet: -0.11 (0.22), residues: 454 loop : -0.90 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.003 0.001 HIS A 655 PHE 0.017 0.001 PHE A 400 TYR 0.024 0.001 TYR C 904 ARG 0.002 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 109 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7479 (ptpp) REVERT: A 229 LEU cc_start: 0.7047 (mt) cc_final: 0.6702 (tt) REVERT: A 368 LEU cc_start: 0.8858 (mp) cc_final: 0.8621 (tp) REVERT: A 441 LEU cc_start: 0.8587 (mt) cc_final: 0.8324 (mp) REVERT: A 559 PHE cc_start: 0.0037 (OUTLIER) cc_final: -0.1595 (m-80) REVERT: A 568 ASP cc_start: 0.6650 (t0) cc_final: 0.6059 (m-30) REVERT: A 947 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8099 (mtmm) REVERT: B 990 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6780 (tm-30) REVERT: C 907 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8704 (t0) outliers start: 46 outliers final: 31 residues processed: 150 average time/residue: 0.2466 time to fit residues: 62.8835 Evaluate side-chains 135 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 225 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 233 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 142 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19680 Z= 0.177 Angle : 0.513 8.614 26768 Z= 0.264 Chirality : 0.043 0.258 3159 Planarity : 0.003 0.037 3427 Dihedral : 5.918 58.789 3192 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.27 % Favored : 95.69 % Rotamer: Outliers : 2.04 % Allowed : 11.04 % Favored : 86.93 % 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: 0.14 (0.17), residues: 2389 helix: 2.02 (0.21), residues: 653 sheet: -0.06 (0.22), residues: 454 loop : -0.88 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 104 HIS 0.003 0.001 HIS A 655 PHE 0.022 0.001 PHE A 392 TYR 0.023 0.001 TYR A 508 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 107 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LEU cc_start: 0.7109 (mt) cc_final: 0.6744 (tt) REVERT: A 441 LEU cc_start: 0.8569 (mt) cc_final: 0.8308 (mp) REVERT: A 568 ASP cc_start: 0.6656 (t0) cc_final: 0.5986 (m-30) REVERT: A 947 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: B 990 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6779 (tm-30) REVERT: C 266 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.5049 (m-80) REVERT: C 907 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8674 (t0) outliers start: 43 outliers final: 32 residues processed: 143 average time/residue: 0.2444 time to fit residues: 59.6982 Evaluate side-chains 134 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 144 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN B 913 GLN B1142 GLN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19680 Z= 0.336 Angle : 0.604 9.080 26768 Z= 0.311 Chirality : 0.046 0.284 3159 Planarity : 0.004 0.035 3427 Dihedral : 6.312 57.938 3192 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 2.18 % Allowed : 11.32 % Favored : 86.50 % 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: -0.18 (0.17), residues: 2389 helix: 1.61 (0.21), residues: 657 sheet: -0.21 (0.22), residues: 455 loop : -1.02 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 104 HIS 0.006 0.001 HIS A 207 PHE 0.030 0.002 PHE A 392 TYR 0.021 0.002 TYR A 508 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 99 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 559 PHE cc_start: 0.0472 (OUTLIER) cc_final: -0.1155 (m-80) REVERT: A 568 ASP cc_start: 0.6426 (t0) cc_final: 0.6154 (t70) REVERT: A 947 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: A 1106 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7839 (pt0) REVERT: B 990 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6948 (tm-30) REVERT: B 1138 TYR cc_start: 0.7238 (t80) cc_final: 0.7036 (t80) REVERT: C 907 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8785 (t0) outliers start: 46 outliers final: 36 residues processed: 138 average time/residue: 0.2418 time to fit residues: 57.7506 Evaluate side-chains 130 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 223 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 170 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 196 optimal weight: 9.9990 chunk 205 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 142 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN A1005 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19680 Z= 0.152 Angle : 0.511 8.133 26768 Z= 0.262 Chirality : 0.044 0.250 3159 Planarity : 0.003 0.037 3427 Dihedral : 5.865 58.480 3192 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.66 % Allowed : 12.22 % Favored : 86.12 % 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: 0.12 (0.17), residues: 2389 helix: 2.03 (0.21), residues: 659 sheet: -0.14 (0.22), residues: 461 loop : -0.90 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.002 0.001 HIS A1064 PHE 0.018 0.001 PHE A 400 TYR 0.020 0.001 TYR C1067 ARG 0.002 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7233 (m-10) cc_final: 0.6877 (m-10) REVERT: A 559 PHE cc_start: 0.0300 (OUTLIER) cc_final: -0.1293 (m-80) REVERT: A 568 ASP cc_start: 0.6345 (t0) cc_final: 0.5748 (m-30) REVERT: A 598 ILE cc_start: 0.8954 (mt) cc_final: 0.8748 (mt) REVERT: A 947 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8075 (mtmm) REVERT: B 990 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6882 (tm-30) REVERT: C 266 TYR cc_start: 0.6054 (OUTLIER) cc_final: 0.5016 (m-80) outliers start: 35 outliers final: 26 residues processed: 132 average time/residue: 0.2545 time to fit residues: 57.2240 Evaluate side-chains 128 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 99 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 229 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 19 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19680 Z= 0.174 Angle : 0.511 8.207 26768 Z= 0.261 Chirality : 0.043 0.250 3159 Planarity : 0.003 0.036 3427 Dihedral : 5.692 57.290 3190 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.56 % Allowed : 12.36 % Favored : 86.07 % 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: 0.12 (0.17), residues: 2389 helix: 2.05 (0.21), residues: 658 sheet: -0.16 (0.22), residues: 471 loop : -0.91 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 104 HIS 0.003 0.001 HIS A 655 PHE 0.017 0.001 PHE A 400 TYR 0.020 0.001 TYR C1067 ARG 0.005 0.000 ARG C 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4778 Ramachandran restraints generated. 2389 Oldfield, 0 Emsley, 2389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 99 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.7250 (m-10) cc_final: 0.6860 (m-10) REVERT: A 559 PHE cc_start: 0.0331 (OUTLIER) cc_final: -0.1280 (m-80) REVERT: A 900 MET cc_start: 0.8164 (mtm) cc_final: 0.7962 (mtp) REVERT: A 947 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (mtmm) REVERT: B 990 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6942 (tm-30) REVERT: C 266 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.5004 (m-80) outliers start: 33 outliers final: 29 residues processed: 128 average time/residue: 0.2462 time to fit residues: 54.4119 Evaluate side-chains 125 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 242 random chunks: chunk 204 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 168 optimal weight: 0.6980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 519 HIS ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.133255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095587 restraints weight = 44366.408| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.39 r_work: 0.3290 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19680 Z= 0.372 Angle : 0.613 7.933 26768 Z= 0.315 Chirality : 0.046 0.282 3159 Planarity : 0.004 0.035 3427 Dihedral : 6.196 57.692 3190 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.89 % Allowed : 12.60 % Favored : 85.50 % 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: -0.24 (0.17), residues: 2389 helix: 1.64 (0.21), residues: 651 sheet: -0.31 (0.22), residues: 465 loop : -1.07 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 104 HIS 0.006 0.001 HIS A1048 PHE 0.021 0.002 PHE A 392 TYR 0.021 0.002 TYR C1067 ARG 0.003 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.88 seconds wall clock time: 64 minutes 5.26 seconds (3845.26 seconds total)