Starting phenix.real_space_refine on Tue Mar 19 10:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/03_2024/7lwl_23549.pdb" } resolution = 2.84 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= 0.097 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 105 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 "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "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: 23847 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "B" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Chain: "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: 12.99, per 1000 atoms: 0.54 Number of scatterers: 23847 At special positions: 0 Unit cell: (135.763, 129.349, 175.316, 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 105 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=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.01 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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: 9.52 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: 74 helices and 49 sheets defined 27.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.727A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.583A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.911A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.950A 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 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.801A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.611A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 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 removed outlier: 3.662A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.143A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.077A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.576A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.652A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.201A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.611A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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 removed outlier: 3.814A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.604A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.610A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.179A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.622A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.602A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.102A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.808A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.091A 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 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.784A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.541A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.805A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 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: 3.580A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.270A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.756A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.088A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.088A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 91 through 96 removed outlier: 4.402A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.989A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.843A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.586A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.660A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.829A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.501A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.107A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.604A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.591A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.993A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.819A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.001A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.430A 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 328 removed outlier: 5.493A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.779A 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 653 through 655 removed outlier: 6.496A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.801A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.696A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.958A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.633A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.138A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.843A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.203A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.943A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.878A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.512A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.813A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.603A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.599A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.500A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.571A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.73 Time building geometry restraints manager: 10.36 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: 6493 1.33 - 1.46: 4441 1.46 - 1.58: 13303 1.58 - 1.70: 0 1.70 - 1.82: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.517 1.544 -0.027 6.70e-03 2.23e+04 1.62e+01 bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.543 -0.026 6.70e-03 2.23e+04 1.56e+01 bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 97.57 - 105.07: 432 105.07 - 112.57: 10962 112.57 - 120.07: 11253 120.07 - 127.57: 10357 127.57 - 135.07: 140 Bond angle restraints: 33144 Sorted by residual: angle pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " pdb=" CG PHE A 86 " ideal model delta sigma weight residual 113.80 121.24 -7.44 1.00e+00 1.00e+00 5.54e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.70 -6.10 1.00e+00 1.00e+00 3.72e+01 angle pdb=" CA PHE A 194 " pdb=" CB PHE A 194 " pdb=" CG PHE A 194 " ideal model delta sigma weight residual 113.80 119.68 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 119.68 -5.88 1.00e+00 1.00e+00 3.45e+01 angle pdb=" CA PHE C 186 " pdb=" CB PHE C 186 " pdb=" CG PHE C 186 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 13907 17.51 - 35.03: 772 35.03 - 52.54: 141 52.54 - 70.06: 56 70.06 - 87.57: 31 Dihedral angle restraints: 14907 sinusoidal: 6180 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -159.53 73.53 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -153.60 67.60 1 1.00e+01 1.00e-02 5.94e+01 dihedral pdb=" CA THR A 599 " pdb=" C THR A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 14904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2465 0.089 - 0.178: 1206 0.178 - 0.268: 178 0.268 - 0.357: 26 0.357 - 0.446: 1 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA THR A 108 " pdb=" N THR A 108 " pdb=" C THR A 108 " pdb=" CB THR A 108 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CA ASP A 745 " pdb=" N ASP A 745 " pdb=" C ASP A 745 " pdb=" CB ASP A 745 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA ASN A 487 " pdb=" N ASN A 487 " pdb=" C ASN A 487 " pdb=" CB ASN A 487 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.141 2.00e-02 2.50e+03 1.50e-01 2.82e+02 pdb=" CG ASN A 603 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.231 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 91 " -0.207 2.00e-02 2.50e+03 1.07e-01 2.30e+02 pdb=" CG TYR A 91 " 0.082 2.00e-02 2.50e+03 pdb=" CD1 TYR A 91 " 0.091 2.00e-02 2.50e+03 pdb=" CD2 TYR A 91 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 TYR A 91 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 91 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 91 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 91 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.122 2.00e-02 2.50e+03 1.26e-01 2.00e+02 pdb=" CG ASN A 709 " 0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.190 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.153 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 11063 2.98 - 3.46: 22327 3.46 - 3.94: 39962 3.94 - 4.42: 44189 4.42 - 4.90: 75325 Nonbonded interactions: 192866 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.505 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.516 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.518 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.527 2.440 ... (remaining 192861 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 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: 7.210 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 68.880 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.077 24366 Z= 0.865 Angle : 1.792 9.099 33144 Z= 1.208 Chirality : 0.096 0.446 3876 Planarity : 0.013 0.158 4251 Dihedral : 12.808 87.572 9168 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.20 % Favored : 95.57 % Rotamer: Outliers : 0.53 % Allowed : 2.14 % Favored : 97.33 % Cbeta Deviations : 0.07 % 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 (0.14), residues: 2955 helix: -0.82 (0.17), residues: 687 sheet: 0.36 (0.22), residues: 505 loop : -0.61 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.022 TRP C 104 HIS 0.009 0.002 HIS A1083 PHE 0.098 0.012 PHE B 718 TYR 0.207 0.022 TYR A 91 ARG 0.010 0.001 ARG C1019 *********************** 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: 14 poor density : 366 time to evaluate : 2.639 Fit side-chains REVERT: A 129 LYS cc_start: 0.6298 (mttm) cc_final: 0.5990 (mppt) REVERT: A 278 LYS cc_start: 0.8327 (tttt) cc_final: 0.8065 (ttpt) REVERT: A 569 ILE cc_start: 0.7914 (mm) cc_final: 0.7711 (mp) REVERT: A 586 ASP cc_start: 0.6859 (t70) cc_final: 0.5886 (m-30) REVERT: A 697 MET cc_start: 0.9140 (ptm) cc_final: 0.8853 (ptm) REVERT: A 731 MET cc_start: 0.9296 (ptt) cc_final: 0.8871 (ptt) REVERT: A 1029 MET cc_start: 0.9294 (tpp) cc_final: 0.8606 (tpp) REVERT: B 32 PHE cc_start: 0.6822 (m-80) cc_final: 0.6382 (m-10) REVERT: B 271 GLN cc_start: 0.7844 (mt0) cc_final: 0.7637 (mm-40) REVERT: B 334 ASN cc_start: 0.6781 (m-40) cc_final: 0.6515 (p0) REVERT: B 357 ARG cc_start: 0.7836 (ttt-90) cc_final: 0.7508 (ttt-90) REVERT: B 359 SER cc_start: 0.8615 (p) cc_final: 0.8189 (m) REVERT: C 81 ASN cc_start: 0.7737 (p0) cc_final: 0.7193 (p0) REVERT: C 121 ASN cc_start: 0.7331 (t0) cc_final: 0.6942 (m-40) REVERT: C 237 ARG cc_start: 0.7971 (mtp-110) cc_final: 0.7740 (mtp85) REVERT: C 369 TYR cc_start: 0.6924 (p90) cc_final: 0.6372 (t80) REVERT: C 378 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7548 (tttp) REVERT: C 403 ARG cc_start: 0.6875 (ptt-90) cc_final: 0.6577 (ptm-80) REVERT: C 405 ASP cc_start: 0.7191 (m-30) cc_final: 0.6496 (m-30) REVERT: C 417 LYS cc_start: 0.8125 (mttt) cc_final: 0.7754 (mmtt) REVERT: C 529 LYS cc_start: 0.8178 (mttt) cc_final: 0.7962 (tppt) REVERT: C 646 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7385 (ttp80) REVERT: C 1017 GLU cc_start: 0.7602 (tt0) cc_final: 0.7364 (tt0) outliers start: 14 outliers final: 6 residues processed: 378 average time/residue: 1.1873 time to fit residues: 521.8992 Evaluate side-chains 215 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 209 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 519 HIS A 755 GLN A 764 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 540 ASN B 607 GLN B 675 GLN B 703 ASN B1010 GLN C 360 ASN C 439 ASN C 506 GLN C 540 ASN C 690 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24366 Z= 0.210 Angle : 0.640 13.102 33144 Z= 0.343 Chirality : 0.047 0.205 3876 Planarity : 0.004 0.041 4251 Dihedral : 6.270 50.709 3838 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.30 % Favored : 97.60 % Rotamer: Outliers : 1.98 % Allowed : 7.55 % Favored : 90.47 % 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: 0.20 (0.15), residues: 2955 helix: 1.22 (0.20), residues: 682 sheet: 0.35 (0.19), residues: 655 loop : -0.38 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 64 HIS 0.006 0.001 HIS B 49 PHE 0.026 0.002 PHE B 453 TYR 0.024 0.002 TYR C 369 ARG 0.006 0.000 ARG B 319 *********************** 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 282 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 230 time to evaluate : 2.828 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6183 (mttm) cc_final: 0.5880 (mppt) REVERT: A 278 LYS cc_start: 0.8381 (tttt) cc_final: 0.8136 (ttmm) REVERT: A 347 PHE cc_start: 0.4712 (OUTLIER) cc_final: 0.4100 (t80) REVERT: A 355 ARG cc_start: 0.7812 (ttt180) cc_final: 0.7594 (tpp80) REVERT: A 569 ILE cc_start: 0.7650 (mm) cc_final: 0.7391 (mm) REVERT: A 586 ASP cc_start: 0.6822 (t70) cc_final: 0.5881 (m-30) REVERT: A 731 MET cc_start: 0.9242 (ptt) cc_final: 0.8927 (ptt) REVERT: A 1029 MET cc_start: 0.9096 (tpp) cc_final: 0.8424 (tpp) REVERT: B 32 PHE cc_start: 0.6616 (m-80) cc_final: 0.6152 (m-10) REVERT: B 323 THR cc_start: 0.8250 (m) cc_final: 0.7749 (p) REVERT: B 357 ARG cc_start: 0.8113 (ttt-90) cc_final: 0.7850 (ttt-90) REVERT: B 359 SER cc_start: 0.8819 (p) cc_final: 0.8302 (m) REVERT: C 81 ASN cc_start: 0.7923 (p0) cc_final: 0.7010 (p0) REVERT: C 188 ASN cc_start: 0.5996 (OUTLIER) cc_final: 0.5273 (p0) REVERT: C 200 TYR cc_start: 0.7950 (m-80) cc_final: 0.7690 (m-80) REVERT: C 205 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8413 (t) REVERT: C 237 ARG cc_start: 0.7808 (mtp180) cc_final: 0.7320 (mtm180) REVERT: C 369 TYR cc_start: 0.7011 (p90) cc_final: 0.6454 (t80) REVERT: C 378 LYS cc_start: 0.7858 (mmtt) cc_final: 0.7498 (tttp) REVERT: C 452 LEU cc_start: 0.8312 (mp) cc_final: 0.7815 (mm) REVERT: C 465 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7258 (mt-10) REVERT: C 505 TYR cc_start: 0.7296 (m-80) cc_final: 0.6780 (t80) REVERT: C 529 LYS cc_start: 0.8101 (mttt) cc_final: 0.7840 (tppt) REVERT: C 574 ASP cc_start: 0.7723 (t70) cc_final: 0.7502 (t0) REVERT: C 1017 GLU cc_start: 0.7533 (tt0) cc_final: 0.7273 (tt0) outliers start: 52 outliers final: 20 residues processed: 268 average time/residue: 1.1222 time to fit residues: 354.4805 Evaluate side-chains 200 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS 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: 0.5980 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 272 optimal weight: 0.6980 chunk 294 optimal weight: 1.9990 chunk 243 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 93 optimal weight: 0.1980 chunk 218 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 914 ASN A1010 GLN A1106 GLN B 49 HIS B 914 ASN B 935 GLN C 207 HIS C 394 ASN C 506 GLN C 804 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24366 Z= 0.173 Angle : 0.566 11.865 33144 Z= 0.296 Chirality : 0.046 0.283 3876 Planarity : 0.004 0.046 4251 Dihedral : 6.185 69.915 3835 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 9.19 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.43 (0.15), residues: 2955 helix: 1.77 (0.21), residues: 686 sheet: 0.30 (0.19), residues: 657 loop : -0.33 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 64 HIS 0.003 0.001 HIS B 49 PHE 0.027 0.001 PHE B 453 TYR 0.022 0.001 TYR C 369 ARG 0.011 0.000 ARG A 403 *********************** 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 259 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 208 time to evaluate : 2.751 Fit side-chains REVERT: A 129 LYS cc_start: 0.6177 (mttm) cc_final: 0.5971 (mppt) REVERT: A 135 PHE cc_start: 0.6348 (t80) cc_final: 0.5990 (t80) REVERT: A 278 LYS cc_start: 0.8427 (tttt) cc_final: 0.8140 (ttmm) REVERT: A 347 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.4053 (t80) REVERT: A 355 ARG cc_start: 0.7873 (ttt180) cc_final: 0.7647 (tpp80) REVERT: A 400 PHE cc_start: 0.6479 (p90) cc_final: 0.5446 (p90) REVERT: A 568 ASP cc_start: 0.6956 (m-30) cc_final: 0.6734 (m-30) REVERT: A 569 ILE cc_start: 0.7670 (mm) cc_final: 0.7360 (mm) REVERT: A 586 ASP cc_start: 0.6889 (t70) cc_final: 0.5871 (m-30) REVERT: A 731 MET cc_start: 0.9246 (ptt) cc_final: 0.8904 (ptt) REVERT: A 1029 MET cc_start: 0.8932 (tpp) cc_final: 0.8484 (tpp) REVERT: B 32 PHE cc_start: 0.6589 (m-80) cc_final: 0.6128 (m-10) REVERT: B 323 THR cc_start: 0.8139 (m) cc_final: 0.7699 (p) REVERT: B 988 GLU cc_start: 0.6896 (mp0) cc_final: 0.6691 (mp0) REVERT: C 81 ASN cc_start: 0.7825 (p0) cc_final: 0.6606 (p0) REVERT: C 200 TYR cc_start: 0.7937 (m-80) cc_final: 0.7556 (m-80) REVERT: C 237 ARG cc_start: 0.7818 (mtp180) cc_final: 0.7393 (mtm180) REVERT: C 239 GLN cc_start: 0.7739 (tt0) cc_final: 0.7120 (tt0) REVERT: C 369 TYR cc_start: 0.6916 (p90) cc_final: 0.6464 (t80) REVERT: C 378 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7447 (tttp) REVERT: C 452 LEU cc_start: 0.8350 (mp) cc_final: 0.7922 (mm) REVERT: C 453 PHE cc_start: 0.7830 (p90) cc_final: 0.7468 (p90) REVERT: C 505 TYR cc_start: 0.7351 (m-80) cc_final: 0.6632 (t80) REVERT: C 506 GLN cc_start: 0.7493 (mt0) cc_final: 0.7245 (mt0) REVERT: C 529 LYS cc_start: 0.8176 (mttt) cc_final: 0.7897 (tppt) REVERT: C 1017 GLU cc_start: 0.7518 (tt0) cc_final: 0.7266 (tt0) outliers start: 51 outliers final: 22 residues processed: 246 average time/residue: 1.0606 time to fit residues: 310.4726 Evaluate side-chains 203 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 180 time to evaluate : 2.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.1980 chunk 205 optimal weight: 3.9990 chunk 141 optimal weight: 0.0870 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 289 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 317 ASN A 354 ASN A 613 GLN A1010 GLN A1106 GLN B 394 ASN B 498 GLN B 501 ASN B 580 GLN B 914 ASN B1010 GLN C 196 ASN C 804 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24366 Z= 0.161 Angle : 0.540 10.435 33144 Z= 0.280 Chirality : 0.045 0.292 3876 Planarity : 0.003 0.047 4251 Dihedral : 6.212 88.678 3835 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.33 % Rotamer: Outliers : 2.02 % Allowed : 9.84 % Favored : 88.14 % 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: 0.54 (0.15), residues: 2955 helix: 2.06 (0.21), residues: 674 sheet: 0.22 (0.19), residues: 650 loop : -0.27 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 PHE 0.029 0.001 PHE B 453 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG A 403 *********************** 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 253 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 2.715 Fit side-chains REVERT: A 84 LEU cc_start: 0.3559 (OUTLIER) cc_final: 0.3278 (mt) REVERT: A 129 LYS cc_start: 0.6225 (mttm) cc_final: 0.5985 (mppt) REVERT: A 135 PHE cc_start: 0.6225 (t80) cc_final: 0.5826 (t80) REVERT: A 278 LYS cc_start: 0.8466 (tttt) cc_final: 0.8118 (ttmm) REVERT: A 355 ARG cc_start: 0.7893 (ttt180) cc_final: 0.7629 (tpp80) REVERT: A 400 PHE cc_start: 0.6485 (p90) cc_final: 0.5925 (p90) REVERT: A 569 ILE cc_start: 0.7731 (mm) cc_final: 0.7460 (mm) REVERT: A 586 ASP cc_start: 0.6785 (t70) cc_final: 0.5747 (m-30) REVERT: A 731 MET cc_start: 0.9269 (ptt) cc_final: 0.8992 (ptt) REVERT: A 1029 MET cc_start: 0.8839 (tpp) cc_final: 0.8331 (tpp) REVERT: B 32 PHE cc_start: 0.6536 (m-80) cc_final: 0.6171 (m-10) REVERT: B 323 THR cc_start: 0.8186 (m) cc_final: 0.7801 (p) REVERT: B 854 LYS cc_start: 0.5229 (mttm) cc_final: 0.5006 (mttm) REVERT: B 957 GLN cc_start: 0.7870 (tt0) cc_final: 0.7622 (tt0) REVERT: B 988 GLU cc_start: 0.6897 (mp0) cc_final: 0.6669 (mp0) REVERT: C 81 ASN cc_start: 0.7824 (p0) cc_final: 0.6586 (p0) REVERT: C 200 TYR cc_start: 0.7893 (m-80) cc_final: 0.7467 (m-80) REVERT: C 237 ARG cc_start: 0.7825 (mtp180) cc_final: 0.7420 (mtm180) REVERT: C 239 GLN cc_start: 0.7721 (tt0) cc_final: 0.7070 (tt0) REVERT: C 281 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: C 369 TYR cc_start: 0.6971 (p90) cc_final: 0.6429 (t80) REVERT: C 378 LYS cc_start: 0.7538 (mmtt) cc_final: 0.7220 (tttp) REVERT: C 453 PHE cc_start: 0.7846 (p90) cc_final: 0.7489 (p90) REVERT: C 505 TYR cc_start: 0.7296 (m-80) cc_final: 0.6654 (t80) REVERT: C 529 LYS cc_start: 0.8194 (mttt) cc_final: 0.7917 (tppt) REVERT: C 740 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8068 (ttt) REVERT: C 994 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7115 (m-30) REVERT: C 1017 GLU cc_start: 0.7524 (tt0) cc_final: 0.7300 (tt0) REVERT: C 1141 LEU cc_start: 0.7886 (tp) cc_final: 0.7685 (tp) REVERT: C 1145 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6564 (mt) outliers start: 53 outliers final: 25 residues processed: 242 average time/residue: 1.0467 time to fit residues: 303.1989 Evaluate side-chains 212 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU 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: 0.3980 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 247 optimal weight: 0.7980 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A 641 ASN A1010 GLN C 196 ASN C 207 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24366 Z= 0.180 Angle : 0.534 11.478 33144 Z= 0.276 Chirality : 0.045 0.235 3876 Planarity : 0.003 0.048 4251 Dihedral : 6.289 96.156 3835 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 10.60 % Favored : 87.26 % 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: 0.55 (0.15), residues: 2955 helix: 2.10 (0.21), residues: 674 sheet: 0.23 (0.19), residues: 637 loop : -0.28 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 64 HIS 0.003 0.001 HIS B 66 PHE 0.030 0.001 PHE B 453 TYR 0.019 0.001 TYR C 170 ARG 0.006 0.000 ARG A1107 *********************** 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 255 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 199 time to evaluate : 2.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6202 (mttm) cc_final: 0.5971 (mppt) REVERT: A 135 PHE cc_start: 0.6246 (t80) cc_final: 0.5796 (t80) REVERT: A 278 LYS cc_start: 0.8476 (tttt) cc_final: 0.8145 (ttmm) REVERT: A 355 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7653 (tpp80) REVERT: A 400 PHE cc_start: 0.6518 (p90) cc_final: 0.6019 (p90) REVERT: A 569 ILE cc_start: 0.7825 (mm) cc_final: 0.7589 (mm) REVERT: A 586 ASP cc_start: 0.6943 (t70) cc_final: 0.5950 (m-30) REVERT: A 603 ASN cc_start: 0.6555 (t0) cc_final: 0.6257 (t0) REVERT: A 731 MET cc_start: 0.9257 (ptt) cc_final: 0.8997 (ptt) REVERT: A 1029 MET cc_start: 0.8863 (tpp) cc_final: 0.8372 (tpp) REVERT: A 1072 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 323 THR cc_start: 0.8166 (m) cc_final: 0.7861 (p) REVERT: B 564 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: B 740 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7423 (ttt) REVERT: B 854 LYS cc_start: 0.5170 (mttm) cc_final: 0.4943 (mttm) REVERT: B 957 GLN cc_start: 0.7866 (tt0) cc_final: 0.7631 (tt0) REVERT: B 988 GLU cc_start: 0.6870 (mp0) cc_final: 0.6652 (mp0) REVERT: C 81 ASN cc_start: 0.7808 (p0) cc_final: 0.6574 (p0) REVERT: C 200 TYR cc_start: 0.7930 (m-80) cc_final: 0.7557 (m-80) REVERT: C 237 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7384 (mtm180) REVERT: C 239 GLN cc_start: 0.7693 (tt0) cc_final: 0.7072 (tt0) REVERT: C 281 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: C 369 TYR cc_start: 0.6915 (p90) cc_final: 0.6447 (t80) REVERT: C 378 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7377 (tttp) REVERT: C 403 ARG cc_start: 0.6729 (ttp80) cc_final: 0.6454 (ttp80) REVERT: C 452 LEU cc_start: 0.8479 (mp) cc_final: 0.7982 (mm) REVERT: C 453 PHE cc_start: 0.7834 (p90) cc_final: 0.7492 (p90) REVERT: C 505 TYR cc_start: 0.7317 (m-80) cc_final: 0.6751 (t80) REVERT: C 529 LYS cc_start: 0.8215 (mttt) cc_final: 0.7938 (tppt) REVERT: C 740 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8111 (ttt) REVERT: C 994 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7136 (m-30) REVERT: C 1017 GLU cc_start: 0.7534 (tt0) cc_final: 0.7304 (tt0) REVERT: C 1141 LEU cc_start: 0.7842 (tp) cc_final: 0.7622 (tp) REVERT: C 1145 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6674 (mt) outliers start: 56 outliers final: 30 residues processed: 242 average time/residue: 1.0876 time to fit residues: 319.2221 Evaluate side-chains 222 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 170 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 290 optimal weight: 4.9990 chunk 240 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A 641 ASN A 901 GLN A1010 GLN B 901 GLN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24366 Z= 0.282 Angle : 0.574 10.616 33144 Z= 0.297 Chirality : 0.047 0.254 3876 Planarity : 0.004 0.049 4251 Dihedral : 6.227 104.221 3835 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.95 % Allowed : 11.56 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2955 helix: 1.97 (0.21), residues: 668 sheet: 0.23 (0.19), residues: 645 loop : -0.41 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 64 HIS 0.004 0.001 HIS B1058 PHE 0.034 0.002 PHE A 541 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG A1039 *********************** 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 233 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 182 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5943 (t80) cc_final: 0.5649 (t80) REVERT: A 278 LYS cc_start: 0.8463 (tttt) cc_final: 0.8120 (ttmm) REVERT: A 355 ARG cc_start: 0.7913 (ttt180) cc_final: 0.7676 (tpp80) REVERT: A 396 TYR cc_start: 0.7495 (m-10) cc_final: 0.7222 (m-10) REVERT: A 400 PHE cc_start: 0.6543 (p90) cc_final: 0.6125 (p90) REVERT: A 569 ILE cc_start: 0.7887 (mm) cc_final: 0.7608 (mm) REVERT: A 586 ASP cc_start: 0.6958 (t70) cc_final: 0.5943 (m-30) REVERT: A 603 ASN cc_start: 0.6717 (t0) cc_final: 0.6379 (t0) REVERT: A 731 MET cc_start: 0.9219 (ptt) cc_final: 0.8941 (ptt) REVERT: A 740 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: A 1029 MET cc_start: 0.8955 (tpp) cc_final: 0.8740 (tpp) REVERT: B 32 PHE cc_start: 0.6148 (m-80) cc_final: 0.5778 (m-10) REVERT: B 323 THR cc_start: 0.8236 (m) cc_final: 0.7908 (p) REVERT: B 564 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6496 (tm-30) REVERT: B 740 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7404 (ttt) REVERT: B 957 GLN cc_start: 0.7890 (tt0) cc_final: 0.7676 (tt0) REVERT: C 81 ASN cc_start: 0.7739 (p0) cc_final: 0.6500 (p0) REVERT: C 200 TYR cc_start: 0.7944 (m-80) cc_final: 0.7655 (m-80) REVERT: C 237 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7223 (mtm110) REVERT: C 239 GLN cc_start: 0.7696 (tt0) cc_final: 0.7074 (tt0) REVERT: C 281 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: C 369 TYR cc_start: 0.6974 (p90) cc_final: 0.6447 (t80) REVERT: C 378 LYS cc_start: 0.7752 (mmtt) cc_final: 0.7458 (tttp) REVERT: C 452 LEU cc_start: 0.8517 (mp) cc_final: 0.8032 (mm) REVERT: C 453 PHE cc_start: 0.7738 (p90) cc_final: 0.7404 (p90) REVERT: C 529 LYS cc_start: 0.8290 (mttt) cc_final: 0.8023 (tppt) REVERT: C 740 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8199 (ttt) REVERT: C 994 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: C 1017 GLU cc_start: 0.7547 (tt0) cc_final: 0.7262 (tt0) outliers start: 51 outliers final: 25 residues processed: 222 average time/residue: 1.0928 time to fit residues: 290.0832 Evaluate side-chains 203 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 289 optimal weight: 0.0670 chunk 180 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A 641 ASN A1010 GLN C 196 ASN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24366 Z= 0.215 Angle : 0.538 11.980 33144 Z= 0.278 Chirality : 0.045 0.250 3876 Planarity : 0.003 0.045 4251 Dihedral : 6.080 111.194 3835 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.88 % Favored : 97.09 % Rotamer: Outliers : 2.06 % Allowed : 11.59 % Favored : 86.35 % 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: 0.44 (0.15), residues: 2955 helix: 2.09 (0.21), residues: 668 sheet: 0.19 (0.19), residues: 654 loop : -0.39 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1064 PHE 0.040 0.001 PHE A 541 TYR 0.022 0.001 TYR C 170 ARG 0.003 0.000 ARG A 403 *********************** 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 247 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 2.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5963 (t80) cc_final: 0.5647 (t80) REVERT: A 278 LYS cc_start: 0.8479 (tttt) cc_final: 0.8107 (ttmm) REVERT: A 355 ARG cc_start: 0.7984 (ttt180) cc_final: 0.7774 (tpp80) REVERT: A 400 PHE cc_start: 0.6548 (p90) cc_final: 0.6177 (p90) REVERT: A 569 ILE cc_start: 0.7943 (mm) cc_final: 0.7677 (mm) REVERT: A 586 ASP cc_start: 0.6925 (t70) cc_final: 0.5933 (m-30) REVERT: A 603 ASN cc_start: 0.6524 (t0) cc_final: 0.6189 (t0) REVERT: A 731 MET cc_start: 0.9246 (ptt) cc_final: 0.8994 (ptt) REVERT: A 935 GLN cc_start: 0.8047 (tt0) cc_final: 0.7847 (tt0) REVERT: B 32 PHE cc_start: 0.6137 (m-80) cc_final: 0.5891 (m-10) REVERT: B 323 THR cc_start: 0.8252 (m) cc_final: 0.7969 (p) REVERT: B 564 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.6551 (tm-30) REVERT: B 740 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7367 (ttt) REVERT: B 900 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: B 902 MET cc_start: 0.8918 (mmm) cc_final: 0.8712 (tpt) REVERT: B 916 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8809 (tp) REVERT: B 957 GLN cc_start: 0.7869 (tt0) cc_final: 0.7647 (tt0) REVERT: C 81 ASN cc_start: 0.7735 (p0) cc_final: 0.6524 (p0) REVERT: C 140 PHE cc_start: 0.7871 (p90) cc_final: 0.7638 (t80) REVERT: C 200 TYR cc_start: 0.7924 (m-80) cc_final: 0.7593 (m-80) REVERT: C 237 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7244 (mtm110) REVERT: C 239 GLN cc_start: 0.7682 (tt0) cc_final: 0.7079 (tt0) REVERT: C 281 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7739 (pm20) REVERT: C 369 TYR cc_start: 0.7015 (p90) cc_final: 0.6470 (t80) REVERT: C 378 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7430 (tttp) REVERT: C 452 LEU cc_start: 0.8545 (mp) cc_final: 0.8059 (mm) REVERT: C 529 LYS cc_start: 0.8322 (mttt) cc_final: 0.7985 (tppt) REVERT: C 740 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8126 (ttt) REVERT: C 994 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: C 1017 GLU cc_start: 0.7555 (tt0) cc_final: 0.7289 (tt0) outliers start: 54 outliers final: 26 residues processed: 233 average time/residue: 1.1050 time to fit residues: 307.1326 Evaluate side-chains 215 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 263 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A 641 ASN A1010 GLN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24366 Z= 0.185 Angle : 0.538 12.300 33144 Z= 0.276 Chirality : 0.045 0.260 3876 Planarity : 0.003 0.045 4251 Dihedral : 5.938 109.233 3835 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 12.01 % Favored : 85.96 % 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: 0.49 (0.15), residues: 2955 helix: 2.14 (0.21), residues: 674 sheet: 0.18 (0.19), residues: 657 loop : -0.36 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.002 0.001 HIS B1058 PHE 0.040 0.001 PHE A 541 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG A 646 *********************** 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 237 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 184 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5983 (t80) cc_final: 0.5651 (t80) REVERT: A 355 ARG cc_start: 0.7851 (ttt180) cc_final: 0.7558 (tpp80) REVERT: A 400 PHE cc_start: 0.6520 (p90) cc_final: 0.6183 (p90) REVERT: A 569 ILE cc_start: 0.7887 (mm) cc_final: 0.7636 (mm) REVERT: A 586 ASP cc_start: 0.6892 (t70) cc_final: 0.5899 (m-30) REVERT: A 731 MET cc_start: 0.9243 (ptt) cc_final: 0.8911 (ptt) REVERT: A 935 GLN cc_start: 0.8053 (tt0) cc_final: 0.7836 (tt0) REVERT: B 32 PHE cc_start: 0.6090 (m-80) cc_final: 0.5863 (m-10) REVERT: B 323 THR cc_start: 0.8260 (m) cc_final: 0.8001 (p) REVERT: B 564 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6505 (tm-30) REVERT: B 740 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7373 (ttt) REVERT: B 900 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8371 (mtm) REVERT: B 902 MET cc_start: 0.8916 (mmm) cc_final: 0.8712 (tpt) REVERT: B 916 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8813 (tp) REVERT: B 957 GLN cc_start: 0.7859 (tt0) cc_final: 0.7659 (tt0) REVERT: C 81 ASN cc_start: 0.7662 (p0) cc_final: 0.6475 (p0) REVERT: C 188 ASN cc_start: 0.5968 (t0) cc_final: 0.5428 (t0) REVERT: C 200 TYR cc_start: 0.7964 (m-80) cc_final: 0.7558 (m-80) REVERT: C 237 ARG cc_start: 0.7853 (mtp180) cc_final: 0.7255 (mtm110) REVERT: C 239 GLN cc_start: 0.7675 (tt0) cc_final: 0.7118 (tt0) REVERT: C 281 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: C 369 TYR cc_start: 0.7021 (p90) cc_final: 0.6475 (t80) REVERT: C 378 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7580 (tttp) REVERT: C 452 LEU cc_start: 0.8547 (mp) cc_final: 0.8063 (mm) REVERT: C 529 LYS cc_start: 0.8323 (mttt) cc_final: 0.7986 (tppt) REVERT: C 740 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: C 994 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7184 (m-30) REVERT: C 1017 GLU cc_start: 0.7536 (tt0) cc_final: 0.7275 (tt0) outliers start: 53 outliers final: 29 residues processed: 222 average time/residue: 1.0872 time to fit residues: 286.9225 Evaluate side-chains 216 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 211 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 268 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 354 ASN A 641 ASN A1010 GLN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 24366 Z= 0.252 Angle : 0.561 13.391 33144 Z= 0.289 Chirality : 0.046 0.268 3876 Planarity : 0.004 0.046 4251 Dihedral : 5.972 107.715 3835 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.94 % Favored : 97.02 % Rotamer: Outliers : 1.87 % Allowed : 12.20 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.15), residues: 2955 helix: 2.02 (0.21), residues: 674 sheet: 0.20 (0.19), residues: 660 loop : -0.43 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.004 0.001 HIS B1058 PHE 0.039 0.002 PHE A 541 TYR 0.023 0.001 TYR C 170 ARG 0.005 0.000 ARG A 567 *********************** 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 233 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 184 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5945 (t80) cc_final: 0.5647 (t80) REVERT: A 354 ASN cc_start: 0.7403 (t0) cc_final: 0.7166 (t0) REVERT: A 400 PHE cc_start: 0.6605 (p90) cc_final: 0.6293 (p90) REVERT: A 569 ILE cc_start: 0.7944 (mm) cc_final: 0.7686 (mm) REVERT: A 586 ASP cc_start: 0.6897 (t70) cc_final: 0.5861 (m-30) REVERT: A 603 ASN cc_start: 0.6563 (t0) cc_final: 0.6213 (t0) REVERT: A 731 MET cc_start: 0.9207 (ptt) cc_final: 0.8954 (ptt) REVERT: A 790 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8409 (ptpp) REVERT: A 935 GLN cc_start: 0.8120 (tt0) cc_final: 0.7912 (tt0) REVERT: B 32 PHE cc_start: 0.6158 (m-80) cc_final: 0.5916 (m-10) REVERT: B 323 THR cc_start: 0.8270 (m) cc_final: 0.8025 (p) REVERT: B 564 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.6511 (tm-30) REVERT: B 740 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7414 (ttt) REVERT: B 900 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8433 (mtm) REVERT: B 957 GLN cc_start: 0.7880 (tt0) cc_final: 0.7659 (tt0) REVERT: C 81 ASN cc_start: 0.7674 (p0) cc_final: 0.6486 (p0) REVERT: C 188 ASN cc_start: 0.5973 (t0) cc_final: 0.5442 (t0) REVERT: C 200 TYR cc_start: 0.7965 (m-80) cc_final: 0.7541 (m-80) REVERT: C 237 ARG cc_start: 0.7857 (mtp180) cc_final: 0.7249 (mtm110) REVERT: C 239 GLN cc_start: 0.7678 (tt0) cc_final: 0.7117 (tt0) REVERT: C 281 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: C 369 TYR cc_start: 0.7110 (p90) cc_final: 0.6488 (t80) REVERT: C 378 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7643 (tttp) REVERT: C 529 LYS cc_start: 0.8342 (mttt) cc_final: 0.8002 (tppt) REVERT: C 740 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8130 (ttt) REVERT: C 994 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: C 1017 GLU cc_start: 0.7564 (tt0) cc_final: 0.7292 (tt0) outliers start: 49 outliers final: 28 residues processed: 221 average time/residue: 1.1066 time to fit residues: 291.9336 Evaluate side-chains 212 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 982 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL 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: 0.9980 chunk 173 optimal weight: 2.9990 chunk 135 optimal weight: 20.0000 chunk 198 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 chunk 237 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 317 ASN A 641 ASN A1010 GLN B 540 ASN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 24366 Z= 0.153 Angle : 0.517 12.906 33144 Z= 0.265 Chirality : 0.045 0.254 3876 Planarity : 0.003 0.043 4251 Dihedral : 5.701 108.920 3835 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer: Outliers : 1.37 % Allowed : 12.85 % Favored : 85.77 % 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: 0.57 (0.15), residues: 2955 helix: 2.28 (0.21), residues: 674 sheet: 0.33 (0.20), residues: 646 loop : -0.39 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.002 0.001 HIS A1088 PHE 0.035 0.001 PHE A 541 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG A 567 ********************** 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 221 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 185 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 PHE cc_start: 0.5911 (t80) cc_final: 0.5553 (t80) REVERT: A 354 ASN cc_start: 0.7503 (t0) cc_final: 0.7228 (t0) REVERT: A 396 TYR cc_start: 0.7017 (m-10) cc_final: 0.6709 (m-10) REVERT: A 400 PHE cc_start: 0.6614 (p90) cc_final: 0.6310 (p90) REVERT: A 569 ILE cc_start: 0.7918 (mm) cc_final: 0.7644 (mm) REVERT: A 586 ASP cc_start: 0.6884 (t70) cc_final: 0.5885 (m-30) REVERT: A 731 MET cc_start: 0.9236 (ptt) cc_final: 0.8969 (ptt) REVERT: A 935 GLN cc_start: 0.7984 (tt0) cc_final: 0.7632 (tt0) REVERT: B 32 PHE cc_start: 0.6146 (m-80) cc_final: 0.5898 (m-10) REVERT: B 564 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: B 740 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7428 (ttt) REVERT: B 900 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8375 (mtm) REVERT: B 916 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8809 (tp) REVERT: C 81 ASN cc_start: 0.7656 (p0) cc_final: 0.6459 (p0) REVERT: C 188 ASN cc_start: 0.6136 (t0) cc_final: 0.5560 (t0) REVERT: C 200 TYR cc_start: 0.7828 (m-80) cc_final: 0.7488 (m-80) REVERT: C 237 ARG cc_start: 0.7828 (mtp180) cc_final: 0.7214 (mtm110) REVERT: C 239 GLN cc_start: 0.7700 (tt0) cc_final: 0.7146 (tt0) REVERT: C 281 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: C 369 TYR cc_start: 0.7046 (p90) cc_final: 0.6471 (t80) REVERT: C 378 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7598 (tttp) REVERT: C 452 LEU cc_start: 0.8585 (mp) cc_final: 0.8063 (mm) REVERT: C 506 GLN cc_start: 0.7533 (mt0) cc_final: 0.7028 (mp10) REVERT: C 529 LYS cc_start: 0.8281 (mttt) cc_final: 0.7940 (tppt) REVERT: C 740 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8027 (ttt) REVERT: C 994 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7118 (m-30) REVERT: C 1017 GLU cc_start: 0.7545 (tt0) cc_final: 0.7291 (tt0) outliers start: 36 outliers final: 20 residues processed: 214 average time/residue: 1.1885 time to fit residues: 298.6585 Evaluate side-chains 205 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 281 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 238 optimal weight: 0.0030 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 317 ASN A 641 ASN A1010 GLN C 207 HIS ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.194134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132212 restraints weight = 28036.105| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.61 r_work: 0.3319 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 24366 Z= 0.191 Angle : 0.528 12.762 33144 Z= 0.271 Chirality : 0.045 0.254 3876 Planarity : 0.003 0.045 4251 Dihedral : 5.653 107.237 3835 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.26 % Allowed : 13.08 % Favored : 85.66 % 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: 0.55 (0.15), residues: 2955 helix: 2.26 (0.21), residues: 674 sheet: 0.30 (0.20), residues: 650 loop : -0.39 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 PHE 0.035 0.001 PHE A 541 TYR 0.024 0.001 TYR C 170 ARG 0.005 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7107.16 seconds wall clock time: 127 minutes 10.70 seconds (7630.70 seconds total)