Starting phenix.real_space_refine (version: dev) on Thu Apr 7 00:35:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/04_2022/7lwl_23549.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/04_2022/7lwl_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_23549/04_2022/7lwl_23549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/04_2022/7lwl_23549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/04_2022/7lwl_23549.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwl_23549/04_2022/7lwl_23549.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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 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 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 chiralities: 10 Time building chain proxies: 12.34, per 1000 atoms: 0.52 Number of scatterers: 23847 At special positions: 0 Unit cell: (133.625, 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 3.4 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: 73 helices and 49 sheets defined 27.0% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.667A 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: 4.780A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.083A 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: 3.778A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.669A 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: 3.673A 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: 4.103A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.022A 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 337 through 343 removed outlier: 3.861A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.682A 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: 4.549A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.208A 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: 3.622A 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: 3.798A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.672A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.756A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.529A 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: 4.281A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.617A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.599A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.080A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.817A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.070A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 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: 3.764A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.572A 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 890 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 939 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.585A 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: 4.336A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.752A 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: 3.977A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 5.651A 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: 3.977A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.722A 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: 6.475A 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: 4.319A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.882A 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: 6.973A 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: 6.549A 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: 3.533A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.322A 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: 5.936A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.500A 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: 4.487A 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: 6.138A 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: 4.621A 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: 7.682A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.015A 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: 4.038A 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: 3.673A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.761A 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: 7.012A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.305A 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: 5.465A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.858A 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: 7.047A 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: 6.477A 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: 6.808A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.021A 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: 3.651A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.378A 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: 5.953A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.597A 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: 4.448A 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: 4.684A 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: 8.046A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.951A 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: 3.787A 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: 5.999A 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: 3.936A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.609A 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: 6.880A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.326A 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: 5.504A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.445A 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: 6.871A 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: 6.560A 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: 6.581A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.645A 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: 6.581A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.468A 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: 4.479A 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: 4.589A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 9.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7077 1.34 - 1.46: 4445 1.46 - 1.59: 12715 1.59 - 1.71: 0 1.71 - 1.84: 129 Bond restraints: 24366 Sorted by residual: bond pdb=" C5 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.435 1.489 -0.054 1.10e-02 8.26e+03 2.42e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.10e-02 8.26e+03 2.35e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.435 1.488 -0.053 1.10e-02 8.26e+03 2.31e+01 bond pdb=" C5 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.10e-02 8.26e+03 2.26e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.10e-02 8.26e+03 2.23e+01 ... (remaining 24361 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.24: 462 105.24 - 112.70: 11236 112.70 - 120.15: 11400 120.15 - 127.60: 9903 127.60 - 135.05: 143 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 113.80 120.55 -6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.00e+00 1.00e+00 3.61e+01 angle pdb=" CA PHE A 238 " pdb=" CB PHE A 238 " pdb=" CG PHE A 238 " ideal model delta sigma weight residual 113.80 119.62 -5.82 1.00e+00 1.00e+00 3.39e+01 angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 119.60 -5.80 1.00e+00 1.00e+00 3.37e+01 angle pdb=" CA ASP B 796 " pdb=" CB ASP B 796 " pdb=" CG ASP B 796 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 ... (remaining 33139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 13446 17.85 - 35.70: 710 35.70 - 53.56: 106 53.56 - 71.41: 47 71.41 - 89.26: 31 Dihedral angle restraints: 14340 sinusoidal: 5613 harmonic: 8727 Sorted by residual: 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 180.00 150.20 29.80 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA THR B 599 " pdb=" C THR B 599 " pdb=" N PRO B 600 " pdb=" CA PRO B 600 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 dihedral pdb=" CA SER A 221 " pdb=" C SER A 221 " pdb=" N ALA A 222 " pdb=" CA ALA A 222 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 14337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2273 0.079 - 0.159: 1343 0.159 - 0.238: 208 0.238 - 0.317: 43 0.317 - 0.397: 9 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA ASN C 487 " pdb=" N ASN C 487 " pdb=" C ASN C 487 " pdb=" CB ASN C 487 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+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 2.14 0.37 2.00e-01 2.50e+01 3.45e+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 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " 0.140 2.00e-02 2.50e+03 1.49e-01 2.79e+02 pdb=" CG ASN A 603 " -0.076 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " -0.230 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " 0.141 2.00e-02 2.50e+03 1.48e-01 2.72e+02 pdb=" CG ASN C 165 " -0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " -0.224 2.00e-02 2.50e+03 pdb=" C1 NAG C1307 " 0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 91 " -0.189 2.00e-02 2.50e+03 9.74e-02 1.90e+02 pdb=" CG TYR A 91 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TYR A 91 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR A 91 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 TYR A 91 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TYR A 91 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR A 91 " -0.018 2.00e-02 2.50e+03 pdb=" OH TYR A 91 " -0.123 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 10937 2.98 - 3.46: 22404 3.46 - 3.94: 40097 3.94 - 4.42: 44014 4.42 - 4.90: 75478 Nonbonded interactions: 192930 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.499 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 2.514 2.440 nonbonded pdb=" OE1 GLU A 516 " pdb=" OH TYR B 200 " model vdw 2.524 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.532 2.440 ... (remaining 192925 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 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. 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: 2.130 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: 8.280 Check model and map are aligned: 0.320 Convert atoms to be neutral: 0.180 Process input model: 61.400 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 0.054 24366 Z= 0.842 Angle : 1.792 9.404 33144 Z= 1.212 Chirality : 0.094 0.397 3876 Planarity : 0.013 0.190 4251 Dihedral : 12.828 89.260 8718 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.30 % Favored : 95.43 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.14 % 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: -0.71 (0.14), residues: 2955 helix: -0.82 (0.17), residues: 697 sheet: 0.53 (0.21), residues: 529 loop : -0.58 (0.14), residues: 1729 *********************** 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 379 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 374 time to evaluate : 2.732 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 377 average time/residue: 1.2143 time to fit residues: 532.3143 Evaluate side-chains 201 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 314 GLN A 354 ASN A 519 HIS A 613 GLN A 641 ASN A 755 GLN A 764 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 271 GLN B 343 ASN B 519 HIS B 675 GLN C 239 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24366 Z= 0.195 Angle : 0.605 7.871 33144 Z= 0.330 Chirality : 0.046 0.196 3876 Planarity : 0.004 0.062 4251 Dihedral : 5.782 26.556 3381 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 2955 helix: 1.23 (0.20), residues: 672 sheet: 0.36 (0.19), residues: 674 loop : -0.41 (0.15), residues: 1609 *********************** 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 267 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 4.097 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 11 residues processed: 257 average time/residue: 1.1662 time to fit residues: 354.6384 Evaluate side-chains 188 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.2182 time to fit residues: 4.7293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 0.0970 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 272 optimal weight: 1.9990 chunk 294 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 907 ASN A 914 ASN A1106 GLN B 394 ASN B 914 ASN B 935 GLN B1010 GLN C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 24366 Z= 0.193 Angle : 0.540 8.666 33144 Z= 0.291 Chirality : 0.044 0.177 3876 Planarity : 0.004 0.072 4251 Dihedral : 5.215 25.091 3381 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer Outliers : 1.68 % 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: 1.66 (0.21), residues: 674 sheet: 0.51 (0.19), residues: 649 loop : -0.40 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 227 average time/residue: 1.0713 time to fit residues: 291.0173 Evaluate side-chains 193 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 2.625 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.2406 time to fit residues: 5.4839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 0.0980 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 A1106 GLN B 66 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN B1010 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 935 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 24366 Z= 0.219 Angle : 0.528 7.865 33144 Z= 0.285 Chirality : 0.047 0.994 3876 Planarity : 0.004 0.071 4251 Dihedral : 5.057 24.931 3381 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.12 % Rotamer Outliers : 2.14 % 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: 0.47 (0.15), residues: 2955 helix: 1.87 (0.21), residues: 663 sheet: 0.57 (0.19), residues: 640 loop : -0.42 (0.14), residues: 1652 *********************** 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 241 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 185 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 27 residues processed: 226 average time/residue: 1.0582 time to fit residues: 288.3283 Evaluate side-chains 194 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 2.430 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 23 residues processed: 4 average time/residue: 0.4949 time to fit residues: 6.1614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 119 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 B 394 ASN B 901 GLN C 207 HIS C 239 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2999 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= 0.224 Angle : 0.525 8.504 33144 Z= 0.281 Chirality : 0.045 0.218 3876 Planarity : 0.004 0.071 4251 Dihedral : 5.033 33.016 3381 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 2955 helix: 1.89 (0.21), residues: 663 sheet: 0.56 (0.20), residues: 640 loop : -0.44 (0.14), residues: 1652 *********************** 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 227 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 177 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 217 average time/residue: 1.0527 time to fit residues: 275.0358 Evaluate side-chains 195 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 2.784 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.3682 time to fit residues: 5.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 290 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24366 Z= 0.213 Angle : 0.517 8.239 33144 Z= 0.276 Chirality : 0.045 0.515 3876 Planarity : 0.004 0.073 4251 Dihedral : 4.914 26.290 3381 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer Outliers : 1.98 % 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: 0.46 (0.15), residues: 2955 helix: 1.94 (0.21), residues: 663 sheet: 0.56 (0.20), residues: 615 loop : -0.45 (0.14), residues: 1677 *********************** 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 227 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 175 time to evaluate : 2.742 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 213 average time/residue: 1.0540 time to fit residues: 271.8206 Evaluate side-chains 188 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 2.736 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.4115 time to fit residues: 4.9861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 165 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 354 ASN A 613 GLN B 394 ASN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24366 Z= 0.201 Angle : 0.510 9.778 33144 Z= 0.271 Chirality : 0.045 0.355 3876 Planarity : 0.004 0.074 4251 Dihedral : 4.800 24.474 3381 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.01 % Favored : 96.95 % Rotamer Outliers : 1.87 % 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: 0.47 (0.15), residues: 2955 helix: 2.01 (0.21), residues: 663 sheet: 0.55 (0.20), residues: 610 loop : -0.46 (0.14), residues: 1682 *********************** 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 226 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 215 average time/residue: 1.0926 time to fit residues: 285.6918 Evaluate side-chains 199 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 2.702 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 0.3172 time to fit residues: 5.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 0.0010 chunk 172 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 613 GLN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 24366 Z= 0.295 Angle : 0.676 59.199 33144 Z= 0.374 Chirality : 0.046 0.352 3876 Planarity : 0.004 0.074 4251 Dihedral : 4.835 24.372 3381 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer Outliers : 1.37 % 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: 0.43 (0.15), residues: 2955 helix: 1.96 (0.21), residues: 663 sheet: 0.53 (0.20), residues: 614 loop : -0.48 (0.14), residues: 1678 *********************** 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 207 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 171 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 201 average time/residue: 1.1041 time to fit residues: 267.3570 Evaluate side-chains 193 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 2.688 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.3790 time to fit residues: 4.3585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.5980 chunk 252 optimal weight: 0.9980 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 254 optimal weight: 0.8980 chunk 268 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 24366 Z= 0.295 Angle : 0.676 59.199 33144 Z= 0.374 Chirality : 0.046 0.352 3876 Planarity : 0.004 0.080 4251 Dihedral : 4.835 24.372 3381 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2955 helix: 1.96 (0.21), residues: 663 sheet: 0.53 (0.20), residues: 614 loop : -0.48 (0.14), residues: 1678 *********************** 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 192 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 192 average time/residue: 1.1478 time to fit residues: 270.0851 Evaluate side-chains 191 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 2.681 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 4.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.5980 chunk 284 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 chunk 198 optimal weight: 2.9990 chunk 298 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 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 354 ASN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 24366 Z= 0.295 Angle : 0.676 59.199 33144 Z= 0.374 Chirality : 0.046 0.352 3876 Planarity : 0.004 0.080 4251 Dihedral : 4.835 24.372 3381 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2955 helix: 1.96 (0.21), residues: 663 sheet: 0.53 (0.20), residues: 614 loop : -0.48 (0.14), residues: 1678 ********************** 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 191 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 2.927 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 191 average time/residue: 1.0912 time to fit residues: 252.0534 Evaluate side-chains 191 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 2.996 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 3.8235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 219 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 238 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN C 188 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.187259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115923 restraints weight = 27724.651| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.12 r_work: 0.3283 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 1.91 restraints_weight: 0.2500 r_work: 0.3246 rms_B_bonded: 1.99 restraints_weight: 0.1250 r_work: 0.3224 rms_B_bonded: 2.14 restraints_weight: 0.0625 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.0312 r_work: 0.3165 rms_B_bonded: 2.76 restraints_weight: 0.0156 r_work: 0.3125 rms_B_bonded: 3.29 restraints_weight: 0.0078 r_work: 0.3075 rms_B_bonded: 4.06 restraints_weight: 0.0039 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 24366 Z= 0.295 Angle : 0.676 59.199 33144 Z= 0.374 Chirality : 0.046 0.352 3876 Planarity : 0.004 0.080 4251 Dihedral : 4.835 24.372 3381 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2955 helix: 1.96 (0.21), residues: 663 sheet: 0.53 (0.20), residues: 614 loop : -0.48 (0.14), residues: 1678 =============================================================================== Job complete usr+sys time: 5682.72 seconds wall clock time: 103 minutes 57.48 seconds (6237.48 seconds total)