Starting phenix.real_space_refine on Tue Mar 19 09:57:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/03_2024/7lwj_23547.pdb" } resolution = 3.24 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= 0.057 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 98 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23840 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7806 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 12.17, per 1000 atoms: 0.51 Number of scatterers: 23840 At special positions: 0 Unit cell: (130.418, 136.832, 167.833, 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 98 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 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=2.02 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 617 " - pdb=" SG CYS C 649 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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 B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " 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 " Time building additional restraints: 8.82 Conformation dependent library (CDL) restraints added in 4.3 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 27.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.825A 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 438 through 443 removed outlier: 3.838A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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: 3.953A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (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 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.735A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.014A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.540A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.610A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.625A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 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 982 removed outlier: 3.850A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1033 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 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.525A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.787A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.771A 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 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 4.510A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.064A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.719A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.683A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.558A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 3.792A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.047A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.021A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.625A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.194A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.901A 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: 4.123A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.711A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.718A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 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 654 through 655 removed outlier: 5.829A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.349A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.322A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.652A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.937A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.922A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.860A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.848A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.083A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.517A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.282A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.632A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.721A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.430A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1011 hydrogen bonds defined for protein. 2718 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: 10.42 Time building geometry restraints manager: 9.67 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: 5580 1.33 - 1.45: 5229 1.45 - 1.58: 13428 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 24359 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24354 not shown) Histogram of bond angle deviations from ideal: 95.48 - 103.41: 230 103.41 - 111.34: 8335 111.34 - 119.27: 10973 119.27 - 127.20: 13394 127.20 - 135.14: 205 Bond angle restraints: 33137 Sorted by residual: angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 120.63 -6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.65 127.42 -5.77 9.40e-01 1.13e+00 3.76e+01 angle pdb=" CA PHE B 59 " pdb=" CB PHE B 59 " pdb=" CG PHE B 59 " ideal model delta sigma weight residual 113.80 119.66 -5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C GLY C 381 " pdb=" N VAL C 382 " pdb=" CA VAL C 382 " ideal model delta sigma weight residual 122.51 130.09 -7.58 1.31e+00 5.83e-01 3.35e+01 angle pdb=" CA PHE A 515 " pdb=" CB PHE A 515 " pdb=" CG PHE A 515 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 ... (remaining 33132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13710 17.79 - 35.59: 939 35.59 - 53.38: 164 53.38 - 71.18: 43 71.18 - 88.97: 29 Dihedral angle restraints: 14885 sinusoidal: 6158 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 176.83 -83.83 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASN C1135 " pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2548 0.097 - 0.193: 1184 0.193 - 0.290: 126 0.290 - 0.387: 16 0.387 - 0.483: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+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 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 917 " 0.224 2.00e-02 2.50e+03 1.29e-01 3.34e+02 pdb=" CG TYR C 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 917 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR C 917 " -0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR C 917 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TYR C 917 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR C 917 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 917 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 917 " 0.221 2.00e-02 2.50e+03 1.27e-01 3.22e+02 pdb=" CG TYR B 917 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 917 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR B 917 " -0.133 2.00e-02 2.50e+03 pdb=" CE1 TYR B 917 " -0.101 2.00e-02 2.50e+03 pdb=" CE2 TYR B 917 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 917 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 917 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.203 2.00e-02 2.50e+03 1.18e-01 2.78e+02 pdb=" CG TYR A 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.187 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 10976 2.97 - 3.45: 23750 3.45 - 3.93: 40331 3.93 - 4.42: 45459 4.42 - 4.90: 76135 Nonbonded interactions: 196651 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.482 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.485 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 2.440 nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.530 2.440 ... (remaining 196646 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 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 1147 or resid 1 \ 301 through 1310)) } 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: 1.200 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: 7.040 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 63.610 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 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 : 0.014 0.079 24359 Z= 0.887 Angle : 1.828 8.438 33137 Z= 1.227 Chirality : 0.098 0.483 3876 Planarity : 0.015 0.174 4251 Dihedral : 13.345 88.970 9161 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.79 % Rotamer: Outliers : 0.84 % Allowed : 3.21 % Favored : 95.95 % Cbeta Deviations : 0.07 % 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: -1.78 (0.14), residues: 2955 helix: -1.30 (0.17), residues: 665 sheet: -0.34 (0.25), residues: 357 loop : -1.34 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.178 0.026 TRP B 886 HIS 0.017 0.003 HIS A1064 PHE 0.101 0.015 PHE A 718 TYR 0.224 0.026 TYR C 917 ARG 0.009 0.001 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 358 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7445 (tp) cc_final: 0.7123 (pp) REVERT: A 347 PHE cc_start: 0.1688 (OUTLIER) cc_final: 0.1016 (t80) REVERT: B 38 TYR cc_start: 0.3781 (m-80) cc_final: 0.2462 (m-80) REVERT: B 329 PHE cc_start: 0.7299 (m-10) cc_final: 0.6870 (m-80) REVERT: C 740 MET cc_start: 0.5971 (tpt) cc_final: 0.5717 (tpt) REVERT: C 900 MET cc_start: 0.6799 (mtp) cc_final: 0.6232 (mtp) REVERT: C 902 MET cc_start: 0.8136 (mmm) cc_final: 0.7909 (tpt) REVERT: C 904 TYR cc_start: 0.7187 (m-80) cc_final: 0.6980 (m-10) outliers start: 22 outliers final: 9 residues processed: 375 average time/residue: 0.3380 time to fit residues: 197.9628 Evaluate side-chains 192 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 182 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 739 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 5.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 272 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B 188 ASN B 343 ASN B 360 ASN B1088 HIS C 314 GLN C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24359 Z= 0.221 Angle : 0.667 9.989 33137 Z= 0.358 Chirality : 0.047 0.240 3876 Planarity : 0.004 0.046 4251 Dihedral : 7.355 58.384 3847 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.91 % Allowed : 8.34 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 2955 helix: 0.15 (0.19), residues: 646 sheet: -0.66 (0.20), residues: 619 loop : -0.98 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 64 HIS 0.007 0.001 HIS C 66 PHE 0.023 0.002 PHE B 855 TYR 0.021 0.002 TYR B 369 ARG 0.005 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7772 (mmtt) cc_final: 0.6922 (mtmm) REVERT: A 347 PHE cc_start: 0.1954 (OUTLIER) cc_final: 0.1192 (t80) REVERT: B 314 GLN cc_start: 0.6662 (mt0) cc_final: 0.6431 (mt0) REVERT: B 365 TYR cc_start: 0.6649 (m-80) cc_final: 0.6272 (m-80) REVERT: B 514 SER cc_start: 0.7438 (m) cc_final: 0.7200 (p) REVERT: C 242 LEU cc_start: 0.6732 (pt) cc_final: 0.6168 (pt) REVERT: C 619 GLU cc_start: 0.5739 (tp30) cc_final: 0.5528 (tp30) REVERT: C 697 MET cc_start: 0.7290 (ptm) cc_final: 0.7071 (ptm) REVERT: C 904 TYR cc_start: 0.7254 (m-80) cc_final: 0.6669 (m-10) outliers start: 50 outliers final: 29 residues processed: 265 average time/residue: 0.3414 time to fit residues: 144.3743 Evaluate side-chains 178 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 148 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 226 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 294 optimal weight: 0.9990 chunk 243 optimal weight: 0.2980 chunk 270 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 24359 Z= 0.193 Angle : 0.602 12.861 33137 Z= 0.315 Chirality : 0.045 0.178 3876 Planarity : 0.004 0.036 4251 Dihedral : 6.673 58.793 3844 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.03 % Allowed : 10.06 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2955 helix: 0.46 (0.20), residues: 647 sheet: -0.62 (0.20), residues: 622 loop : -0.79 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.005 0.001 HIS C1048 PHE 0.018 0.002 PHE B 86 TYR 0.018 0.002 TYR A 369 ARG 0.006 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 186 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.2305 (OUTLIER) cc_final: 0.1514 (t80) REVERT: A 904 TYR cc_start: 0.4749 (m-10) cc_final: 0.4107 (m-80) REVERT: B 242 LEU cc_start: 0.6122 (mm) cc_final: 0.5798 (tp) REVERT: B 365 TYR cc_start: 0.6623 (m-80) cc_final: 0.6251 (m-80) REVERT: B 514 SER cc_start: 0.7393 (m) cc_final: 0.7135 (p) REVERT: B 577 ARG cc_start: 0.6837 (ttp80) cc_final: 0.6218 (ptm160) REVERT: B 664 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6423 (tp) REVERT: C 242 LEU cc_start: 0.6906 (pt) cc_final: 0.6521 (pt) REVERT: C 396 TYR cc_start: 0.5385 (m-10) cc_final: 0.5163 (m-80) REVERT: C 564 GLN cc_start: 0.6622 (mt0) cc_final: 0.6347 (mt0) REVERT: C 619 GLU cc_start: 0.5760 (tp30) cc_final: 0.5437 (tp30) REVERT: C 902 MET cc_start: 0.8213 (tpp) cc_final: 0.7905 (tpt) REVERT: C 904 TYR cc_start: 0.7182 (m-80) cc_final: 0.6533 (m-10) outliers start: 53 outliers final: 29 residues processed: 233 average time/residue: 0.3366 time to fit residues: 126.6586 Evaluate side-chains 177 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 655 HIS A 762 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 334 ASN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24359 Z= 0.326 Angle : 0.647 10.888 33137 Z= 0.339 Chirality : 0.047 0.188 3876 Planarity : 0.004 0.042 4251 Dihedral : 6.668 59.563 3840 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.75 % Allowed : 11.01 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.15), residues: 2955 helix: 0.07 (0.19), residues: 654 sheet: -0.59 (0.20), residues: 604 loop : -0.93 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 64 HIS 0.007 0.001 HIS A 66 PHE 0.027 0.002 PHE A 275 TYR 0.022 0.002 TYR C1067 ARG 0.006 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 155 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7682 (mmmt) REVERT: A 347 PHE cc_start: 0.2317 (OUTLIER) cc_final: 0.1646 (t80) REVERT: A 759 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.4880 (m-80) REVERT: A 996 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8849 (tt) REVERT: B 242 LEU cc_start: 0.6092 (mm) cc_final: 0.5865 (tp) REVERT: B 560 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6629 (mt) REVERT: B 577 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6313 (ptm160) REVERT: C 242 LEU cc_start: 0.6981 (pt) cc_final: 0.6719 (pt) REVERT: C 759 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.5892 (m-10) REVERT: C 902 MET cc_start: 0.8418 (tpp) cc_final: 0.8184 (tpt) REVERT: C 904 TYR cc_start: 0.7360 (m-80) cc_final: 0.6745 (m-10) outliers start: 72 outliers final: 48 residues processed: 218 average time/residue: 0.3232 time to fit residues: 114.1836 Evaluate side-chains 189 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 136 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 0.0470 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 992 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24359 Z= 0.205 Angle : 0.572 11.571 33137 Z= 0.296 Chirality : 0.044 0.168 3876 Planarity : 0.004 0.124 4251 Dihedral : 6.304 59.695 3836 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.56 % Allowed : 12.01 % Favored : 85.43 % 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: -0.77 (0.15), residues: 2955 helix: 0.43 (0.20), residues: 654 sheet: -0.53 (0.20), residues: 592 loop : -0.85 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 PHE 0.019 0.001 PHE A 275 TYR 0.019 0.002 TYR C 170 ARG 0.008 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 152 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7711 (mmmt) REVERT: A 347 PHE cc_start: 0.2469 (OUTLIER) cc_final: 0.1750 (t80) REVERT: B 360 ASN cc_start: 0.6421 (t0) cc_final: 0.6209 (t0) REVERT: B 365 TYR cc_start: 0.6672 (m-80) cc_final: 0.6325 (m-80) REVERT: B 577 ARG cc_start: 0.7062 (ttp80) cc_final: 0.6435 (ptm160) REVERT: B 873 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: C 242 LEU cc_start: 0.6816 (pt) cc_final: 0.6591 (pt) REVERT: C 564 GLN cc_start: 0.6301 (mt0) cc_final: 0.5914 (mt0) REVERT: C 759 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5748 (m-10) REVERT: C 904 TYR cc_start: 0.7383 (m-80) cc_final: 0.6706 (m-10) outliers start: 67 outliers final: 46 residues processed: 210 average time/residue: 0.3074 time to fit residues: 106.9757 Evaluate side-chains 193 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 290 optimal weight: 0.6980 chunk 240 optimal weight: 0.6980 chunk 134 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24359 Z= 0.206 Angle : 0.565 11.607 33137 Z= 0.291 Chirality : 0.044 0.162 3876 Planarity : 0.004 0.058 4251 Dihedral : 5.996 59.645 3836 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.98 % Allowed : 11.74 % Favored : 85.28 % 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: -0.70 (0.15), residues: 2955 helix: 0.53 (0.20), residues: 654 sheet: -0.46 (0.21), residues: 590 loop : -0.84 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 64 HIS 0.006 0.001 HIS C1048 PHE 0.020 0.001 PHE B 562 TYR 0.018 0.002 TYR C1067 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 152 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.2258 (OUTLIER) cc_final: 0.1657 (t80) REVERT: A 759 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.5120 (m-80) REVERT: B 360 ASN cc_start: 0.6562 (t0) cc_final: 0.6309 (t0) REVERT: B 365 TYR cc_start: 0.6704 (m-80) cc_final: 0.6359 (m-80) REVERT: B 577 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6336 (ptm160) REVERT: B 873 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7726 (m-10) REVERT: C 213 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7790 (t) REVERT: C 564 GLN cc_start: 0.6226 (mt0) cc_final: 0.5897 (mt0) REVERT: C 759 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.5744 (m-10) REVERT: C 904 TYR cc_start: 0.7388 (m-80) cc_final: 0.6751 (m-10) outliers start: 78 outliers final: 49 residues processed: 217 average time/residue: 0.3184 time to fit residues: 114.0905 Evaluate side-chains 192 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 180 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24359 Z= 0.406 Angle : 0.683 10.580 33137 Z= 0.354 Chirality : 0.048 0.221 3876 Planarity : 0.005 0.141 4251 Dihedral : 6.457 59.710 3836 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.14 % Allowed : 12.24 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2955 helix: -0.02 (0.19), residues: 661 sheet: -0.64 (0.20), residues: 595 loop : -1.10 (0.14), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 64 HIS 0.006 0.001 HIS C1048 PHE 0.030 0.002 PHE C 823 TYR 0.026 0.002 TYR C1067 ARG 0.009 0.001 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 142 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.2394 (OUTLIER) cc_final: 0.1776 (t80) REVERT: A 480 CYS cc_start: 0.2005 (OUTLIER) cc_final: 0.0356 (t) REVERT: A 759 PHE cc_start: 0.5390 (OUTLIER) cc_final: 0.5074 (m-80) REVERT: A 873 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: B 577 ARG cc_start: 0.6948 (ttp80) cc_final: 0.6272 (ptm160) REVERT: B 664 ILE cc_start: 0.6889 (OUTLIER) cc_final: 0.6494 (tp) REVERT: B 873 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7745 (m-10) REVERT: C 213 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7702 (t) REVERT: C 564 GLN cc_start: 0.6314 (mt0) cc_final: 0.5988 (mt0) REVERT: C 759 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.5914 (m-10) REVERT: C 904 TYR cc_start: 0.7517 (m-80) cc_final: 0.6862 (m-10) outliers start: 82 outliers final: 59 residues processed: 214 average time/residue: 0.3163 time to fit residues: 112.3039 Evaluate side-chains 199 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 132 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.6980 chunk 115 optimal weight: 10.0000 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B1002 GLN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24359 Z= 0.219 Angle : 0.584 11.385 33137 Z= 0.301 Chirality : 0.044 0.197 3876 Planarity : 0.004 0.089 4251 Dihedral : 6.194 59.593 3836 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.64 % Allowed : 13.19 % Favored : 84.17 % 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: -0.97 (0.15), residues: 2955 helix: 0.15 (0.19), residues: 670 sheet: -0.58 (0.21), residues: 593 loop : -0.97 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.026 0.001 PHE B 392 TYR 0.024 0.002 TYR C 28 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 147 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 PHE cc_start: 0.2316 (OUTLIER) cc_final: 0.1696 (t80) REVERT: A 480 CYS cc_start: 0.1805 (OUTLIER) cc_final: 0.0461 (t) REVERT: A 759 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: B 577 ARG cc_start: 0.6799 (ttp80) cc_final: 0.6164 (ptm160) REVERT: B 873 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7737 (m-10) REVERT: C 564 GLN cc_start: 0.6125 (mt0) cc_final: 0.5870 (mt0) REVERT: C 759 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.5807 (m-10) REVERT: C 904 TYR cc_start: 0.7409 (m-80) cc_final: 0.6822 (m-10) outliers start: 69 outliers final: 53 residues processed: 207 average time/residue: 0.3264 time to fit residues: 112.0144 Evaluate side-chains 197 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 139 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 269 optimal weight: 0.9990 chunk 276 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 243 optimal weight: 0.1980 chunk 254 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24359 Z= 0.171 Angle : 0.555 11.890 33137 Z= 0.284 Chirality : 0.044 0.193 3876 Planarity : 0.004 0.064 4251 Dihedral : 5.693 59.286 3836 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.45 % Allowed : 13.80 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2955 helix: 0.38 (0.19), residues: 670 sheet: -0.50 (0.21), residues: 583 loop : -0.82 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.025 0.001 PHE B 562 TYR 0.017 0.001 TYR B 369 ARG 0.006 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 154 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.5403 (OUTLIER) cc_final: 0.5024 (p) REVERT: A 347 PHE cc_start: 0.2363 (OUTLIER) cc_final: 0.1762 (t80) REVERT: A 480 CYS cc_start: 0.1766 (OUTLIER) cc_final: 0.1033 (p) REVERT: A 759 PHE cc_start: 0.5510 (OUTLIER) cc_final: 0.5112 (m-80) REVERT: A 873 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6047 (m-80) REVERT: A 1050 MET cc_start: 0.5858 (ptp) cc_final: 0.5585 (ptp) REVERT: B 357 ARG cc_start: 0.6368 (ttp80) cc_final: 0.5970 (ttp-110) REVERT: B 577 ARG cc_start: 0.6756 (ttp80) cc_final: 0.6115 (ptm160) REVERT: B 664 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6484 (tp) REVERT: B 873 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7685 (m-10) REVERT: C 64 TRP cc_start: 0.7183 (t60) cc_final: 0.6912 (t60) REVERT: C 759 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5710 (m-10) REVERT: C 904 TYR cc_start: 0.7365 (m-80) cc_final: 0.6712 (m-10) REVERT: C 1077 THR cc_start: 0.5590 (OUTLIER) cc_final: 0.4735 (t) outliers start: 64 outliers final: 45 residues processed: 206 average time/residue: 0.3199 time to fit residues: 109.1995 Evaluate side-chains 194 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 298 optimal weight: 5.9990 chunk 275 optimal weight: 0.4980 chunk 237 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 0.4980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 969 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 66 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24359 Z= 0.204 Angle : 0.572 13.933 33137 Z= 0.291 Chirality : 0.044 0.279 3876 Planarity : 0.004 0.062 4251 Dihedral : 5.580 59.214 3834 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.33 % Allowed : 14.15 % Favored : 83.52 % 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: -0.78 (0.15), residues: 2955 helix: 0.30 (0.20), residues: 668 sheet: -0.50 (0.21), residues: 594 loop : -0.82 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.025 0.001 PHE B 562 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 137 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7808 (mmmt) REVERT: A 63 THR cc_start: 0.5398 (OUTLIER) cc_final: 0.5009 (p) REVERT: A 298 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.5182 (tp30) REVERT: A 347 PHE cc_start: 0.2339 (OUTLIER) cc_final: 0.1761 (t80) REVERT: A 480 CYS cc_start: 0.1710 (OUTLIER) cc_final: 0.0944 (p) REVERT: A 873 TYR cc_start: 0.6922 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: B 357 ARG cc_start: 0.6408 (ttp80) cc_final: 0.5993 (ttp-110) REVERT: B 577 ARG cc_start: 0.6800 (ttp80) cc_final: 0.6142 (ptm160) REVERT: B 664 ILE cc_start: 0.6795 (OUTLIER) cc_final: 0.6477 (tp) REVERT: B 873 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.7628 (m-10) REVERT: C 64 TRP cc_start: 0.7168 (t60) cc_final: 0.6843 (t60) REVERT: C 759 PHE cc_start: 0.6966 (OUTLIER) cc_final: 0.5737 (m-10) REVERT: C 904 TYR cc_start: 0.7371 (m-80) cc_final: 0.6718 (m-10) outliers start: 61 outliers final: 50 residues processed: 187 average time/residue: 0.3228 time to fit residues: 99.6792 Evaluate side-chains 187 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 651 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1098 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 3.9990 chunk 253 optimal weight: 0.0670 chunk 72 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 238 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 30 optimal weight: 20.0000 chunk 43 optimal weight: 0.7980 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 856 ASN B1011 GLN ** C 317 ASN ** 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 = 0.4658 r_free = 0.4658 target = 0.193787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.163725 restraints weight = 45681.616| |-----------------------------------------------------------------------------| r_work (start): 0.4312 rms_B_bonded: 3.92 r_work: 0.3982 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 24359 Z= 0.154 Angle : 0.540 11.707 33137 Z= 0.275 Chirality : 0.043 0.264 3876 Planarity : 0.004 0.044 4251 Dihedral : 5.235 59.278 3834 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.87 % Allowed : 14.65 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 2955 helix: 0.49 (0.20), residues: 668 sheet: -0.49 (0.21), residues: 601 loop : -0.68 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 PHE 0.024 0.001 PHE B 562 TYR 0.019 0.001 TYR C1067 ARG 0.006 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4507.20 seconds wall clock time: 82 minutes 46.16 seconds (4966.16 seconds total)