Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 10 05:32:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lwj_23547/05_2023/7lwj_23547.pdb" } resolution = 3.24 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= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 15204 2.51 5 N 3924 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 23840 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 7807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7807 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7806 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 47, 'TRANS': 953} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen 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: 11.75, per 1000 atoms: 0.49 Number of scatterers: 23840 At special positions: 0 Unit cell: (130.418, 136.832, 167.833, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 4614 8.00 N 3924 7.00 C 15204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.06 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 122 " " NAG B1306 " - " ASN B 282 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 122 " Time building additional restraints: 9.94 Conformation dependent library (CDL) restraints added in 3.6 seconds 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 51 sheets defined 27.1% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.900A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.825A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.838A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.953A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.735A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 4.014A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.540A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.610A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.625A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.850A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1033 Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.525A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.584A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.787A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.771A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 4.510A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.538A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.064A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.719A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.683A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.558A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.989A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 986 through 1033 removed outlier: 3.792A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.047A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.021A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.625A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.194A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.123A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.422A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.711A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.718A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.829A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.349A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.322A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.423A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.531A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.652A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.937A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.826A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.922A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.860A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.569A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.961A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.605A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.603A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.801A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.848A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 141 through 142 removed outlier: 6.083A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.517A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 318 through 319 Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.532A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.282A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.632A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.892A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.721A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.430A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.367A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1011 hydrogen bonds defined for protein. 2718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.22 Time building geometry restraints manager: 10.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5580 1.33 - 1.45: 5229 1.45 - 1.58: 13428 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 24359 Sorted by residual: bond pdb=" CA PRO C 862 " pdb=" C PRO C 862 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.492 -0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C5 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C5 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 24354 not shown) Histogram of bond angle deviations from ideal: 95.48 - 103.41: 230 103.41 - 111.34: 8335 111.34 - 119.27: 10973 119.27 - 127.20: 13394 127.20 - 135.14: 205 Bond angle restraints: 33137 Sorted by residual: angle pdb=" CA PHE C 275 " pdb=" CB PHE C 275 " pdb=" CG PHE C 275 " ideal model delta sigma weight residual 113.80 120.63 -6.83 1.00e+00 1.00e+00 4.67e+01 angle pdb=" C GLY C 594 " pdb=" N VAL C 595 " pdb=" CA VAL C 595 " ideal model delta sigma weight residual 121.65 127.42 -5.77 9.40e-01 1.13e+00 3.76e+01 angle pdb=" CA PHE B 59 " pdb=" CB PHE B 59 " pdb=" CG PHE B 59 " ideal model delta sigma weight residual 113.80 119.66 -5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" C GLY C 381 " pdb=" N VAL C 382 " pdb=" CA VAL C 382 " ideal model delta sigma weight residual 122.51 130.09 -7.58 1.31e+00 5.83e-01 3.35e+01 angle pdb=" CA PHE A 515 " pdb=" CB PHE A 515 " pdb=" CG PHE A 515 " ideal model delta sigma weight residual 113.80 119.49 -5.69 1.00e+00 1.00e+00 3.24e+01 ... (remaining 33132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13118 17.79 - 35.59: 921 35.59 - 53.38: 144 53.38 - 71.18: 43 71.18 - 88.97: 29 Dihedral angle restraints: 14255 sinusoidal: 5528 harmonic: 8727 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 176.83 -83.83 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA THR B 95 " pdb=" C THR B 95 " pdb=" N GLU B 96 " pdb=" CA GLU B 96 " ideal model delta harmonic sigma weight residual -180.00 -149.97 -30.03 0 5.00e+00 4.00e-02 3.61e+01 dihedral pdb=" CA ASN C1135 " pdb=" C ASN C1135 " pdb=" N THR C1136 " pdb=" CA THR C1136 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 14252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2548 0.097 - 0.193: 1184 0.193 - 0.290: 126 0.290 - 0.387: 16 0.387 - 0.483: 2 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA GLU A 773 " pdb=" N GLU A 773 " pdb=" C GLU A 773 " pdb=" CB GLU A 773 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA GLU C 773 " pdb=" N GLU C 773 " pdb=" C GLU C 773 " pdb=" CB GLU C 773 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA ASP B1041 " pdb=" N ASP B1041 " pdb=" C ASP B1041 " pdb=" CB ASP B1041 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 3873 not shown) Planarity restraints: 4281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 917 " 0.224 2.00e-02 2.50e+03 1.29e-01 3.34e+02 pdb=" CG TYR C 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 917 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR C 917 " -0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR C 917 " -0.104 2.00e-02 2.50e+03 pdb=" CE2 TYR C 917 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR C 917 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 917 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 917 " 0.221 2.00e-02 2.50e+03 1.27e-01 3.22e+02 pdb=" CG TYR B 917 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR B 917 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR B 917 " -0.133 2.00e-02 2.50e+03 pdb=" CE1 TYR B 917 " -0.101 2.00e-02 2.50e+03 pdb=" CE2 TYR B 917 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR B 917 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 917 " 0.197 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.203 2.00e-02 2.50e+03 1.18e-01 2.78e+02 pdb=" CG TYR A 917 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.124 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.056 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.187 2.00e-02 2.50e+03 ... (remaining 4278 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 10976 2.97 - 3.45: 23750 3.45 - 3.93: 40331 3.93 - 4.42: 45459 4.42 - 4.90: 76135 Nonbonded interactions: 196651 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.482 2.440 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.485 2.440 nonbonded pdb=" OH TYR A 200 " pdb=" OE2 GLU C 516 " model vdw 2.519 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.523 2.440 nonbonded pdb=" OG SER C 813 " pdb=" OE1 GLU C 868 " model vdw 2.530 2.440 ... (remaining 196646 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 479 or (resid 480 and (name N or name CA or nam \ e C or name O or name CB )) or resid 481 through 487 or (resid 488 and (name N o \ r name CA or name C or name O or name CB )) or resid 489 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 589 or (resid 5 \ 90 and (name N or name CA or name C or name O or name CB )) or resid 591 through \ 1147 or resid 1301 through 1310)) selection = (chain 'C' and (resid 27 through 360 or (resid 361 and (name N or name CA or nam \ e C or name O or name CB )) or resid 362 through 390 or (resid 391 and (name N o \ r name CA or name C or name O or name CB )) or resid 392 through 1147 or resid 1 \ 301 through 1310)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.010 Extract box with map and model: 8.130 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 66.150 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.120 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.014 0.079 24359 Z= 0.887 Angle : 1.828 8.438 33137 Z= 1.227 Chirality : 0.098 0.483 3876 Planarity : 0.015 0.174 4251 Dihedral : 13.550 88.970 8531 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 0.34 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.01 % Favored : 92.79 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 2955 helix: -1.30 (0.17), residues: 665 sheet: -0.34 (0.25), residues: 357 loop : -1.34 (0.13), residues: 1933 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5910 Ramachandran restraints generated. 2955 Oldfield, 0 Emsley, 2955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 358 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 375 average time/residue: 0.3649 time to fit residues: 213.6885 Evaluate side-chains 190 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 2.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2771 time to fit residues: 8.1822 ------------------------------------------------------------------------------- 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: 5.9990 chunk 227 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 30.0000 chunk 90 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 175 optimal weight: 0.5980 chunk 272 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B 188 ASN B 343 ASN B 360 ASN B1088 HIS C 314 GLN C1113 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6631 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 24359 Z= 0.225 Angle : 0.680 10.261 33137 Z= 0.365 Chirality : 0.047 0.237 3876 Planarity : 0.004 0.049 4251 Dihedral : 6.488 29.599 3201 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 2955 helix: 0.03 (0.19), residues: 652 sheet: -0.66 (0.20), residues: 599 loop : -1.03 (0.14), residues: 1704 *********************** 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 263 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 257 average time/residue: 0.3611 time to fit residues: 148.0200 Evaluate side-chains 177 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 2.938 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2199 time to fit residues: 13.3208 ------------------------------------------------------------------------------- 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: 0.7980 chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 30.0000 chunk 185 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 272 optimal weight: 2.9990 chunk 294 optimal weight: 0.8980 chunk 243 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN B 314 GLN B 360 ASN B1011 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 24359 Z= 0.228 Angle : 0.627 12.726 33137 Z= 0.327 Chirality : 0.046 0.233 3876 Planarity : 0.004 0.039 4251 Dihedral : 5.771 26.215 3201 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.11 % 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: -0.88 (0.15), residues: 2955 helix: 0.33 (0.20), residues: 646 sheet: -0.68 (0.20), residues: 634 loop : -0.87 (0.15), residues: 1675 *********************** 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 209 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 180 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 206 average time/residue: 0.3714 time to fit residues: 124.1828 Evaluate side-chains 153 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 2.839 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2181 time to fit residues: 9.3220 ------------------------------------------------------------------------------- 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: 0.9980 chunk 205 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 273 optimal weight: 0.9990 chunk 289 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 chunk 259 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 762 GLN ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 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: 0.6730 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 24359 Z= 0.285 Angle : 0.635 12.873 33137 Z= 0.330 Chirality : 0.046 0.204 3876 Planarity : 0.004 0.038 4251 Dihedral : 5.535 25.358 3201 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: -0.95 (0.15), residues: 2955 helix: 0.15 (0.19), residues: 655 sheet: -0.66 (0.20), residues: 615 loop : -0.90 (0.15), residues: 1685 *********************** 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 202 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 3.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 24 residues processed: 197 average time/residue: 0.3499 time to fit residues: 112.8477 Evaluate side-chains 165 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 3.072 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2224 time to fit residues: 14.3693 ------------------------------------------------------------------------------- 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: 0.1980 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.091 24359 Z= 0.364 Angle : 0.673 10.998 33137 Z= 0.347 Chirality : 0.047 0.184 3876 Planarity : 0.004 0.043 4251 Dihedral : 5.591 25.589 3201 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -1.14 (0.15), residues: 2955 helix: 0.04 (0.19), residues: 652 sheet: -0.69 (0.20), residues: 597 loop : -1.09 (0.14), residues: 1706 *********************** 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 183 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 14 residues processed: 177 average time/residue: 0.3405 time to fit residues: 99.0814 Evaluate side-chains 148 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 2.762 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2185 time to fit residues: 9.6523 ------------------------------------------------------------------------------- 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: 0.6980 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 290 optimal weight: 0.5980 chunk 240 optimal weight: 0.5980 chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 949 GLN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 360 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 24359 Z= 0.181 Angle : 0.579 11.452 33137 Z= 0.296 Chirality : 0.044 0.401 3876 Planarity : 0.004 0.048 4251 Dihedral : 5.205 21.926 3201 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -0.84 (0.15), residues: 2955 helix: 0.43 (0.20), residues: 655 sheet: -0.58 (0.20), residues: 603 loop : -0.93 (0.15), residues: 1697 *********************** 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 181 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 157 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 174 average time/residue: 0.3377 time to fit residues: 97.9777 Evaluate side-chains 155 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2419 time to fit residues: 8.9844 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 30.0000 chunk 165 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1088 HIS C 196 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.098 24359 Z= 0.523 Angle : 0.759 12.626 33137 Z= 0.392 Chirality : 0.051 0.262 3876 Planarity : 0.005 0.109 4251 Dihedral : 5.746 26.384 3201 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 2955 helix: -0.27 (0.19), residues: 662 sheet: -0.82 (0.20), residues: 619 loop : -1.28 (0.14), residues: 1674 *********************** 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 181 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 3.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 175 average time/residue: 0.3523 time to fit residues: 101.0172 Evaluate side-chains 156 residues out of total 2622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 2.813 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2227 time to fit residues: 13.4417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2379 > 50: distance: 61 - 78: 23.193 distance: 65 - 84: 22.468 distance: 74 - 78: 22.445 distance: 75 - 100: 30.728 distance: 78 - 79: 22.882 distance: 79 - 80: 46.885 distance: 79 - 82: 30.110 distance: 80 - 81: 58.031 distance: 80 - 84: 40.004 distance: 81 - 108: 41.393 distance: 82 - 83: 29.062 distance: 84 - 85: 30.831 distance: 85 - 86: 34.676 distance: 85 - 88: 17.097 distance: 86 - 87: 36.857 distance: 86 - 92: 31.694 distance: 88 - 89: 12.417 distance: 89 - 90: 24.361 distance: 89 - 91: 21.011 distance: 92 - 93: 28.640 distance: 93 - 94: 15.873 distance: 93 - 96: 43.986 distance: 94 - 95: 21.741 distance: 94 - 100: 32.301 distance: 96 - 97: 21.290 distance: 97 - 98: 40.090 distance: 97 - 99: 36.068 distance: 100 - 101: 40.039 distance: 101 - 102: 22.650 distance: 101 - 104: 42.230 distance: 102 - 103: 43.661 distance: 102 - 108: 41.481 distance: 104 - 105: 15.539 distance: 105 - 106: 45.018 distance: 105 - 107: 52.895 distance: 108 - 109: 15.217 distance: 109 - 110: 32.582 distance: 109 - 112: 22.828 distance: 110 - 111: 4.545 distance: 110 - 116: 34.489 distance: 112 - 113: 25.540 distance: 113 - 114: 21.248 distance: 113 - 115: 17.180 distance: 116 - 117: 22.761 distance: 117 - 118: 60.311 distance: 117 - 120: 11.283 distance: 118 - 119: 58.992 distance: 118 - 125: 4.625 distance: 120 - 121: 31.909 distance: 121 - 122: 21.484 distance: 122 - 124: 3.840 distance: 125 - 126: 34.858 distance: 126 - 127: 45.605 distance: 126 - 129: 38.394 distance: 127 - 128: 50.430 distance: 127 - 137: 34.620 distance: 129 - 130: 25.071 distance: 130 - 131: 7.524 distance: 130 - 132: 10.099 distance: 131 - 133: 18.652 distance: 132 - 134: 11.512 distance: 133 - 135: 3.445 distance: 134 - 135: 10.796 distance: 135 - 136: 10.206 distance: 137 - 138: 18.995 distance: 138 - 139: 39.257 distance: 139 - 140: 35.546 distance: 139 - 141: 17.139 distance: 141 - 142: 19.653 distance: 142 - 143: 13.512 distance: 142 - 145: 41.265 distance: 143 - 144: 43.867 distance: 143 - 147: 11.740 distance: 144 - 169: 27.033 distance: 145 - 146: 25.054 distance: 147 - 148: 20.121 distance: 148 - 149: 14.003 distance: 148 - 151: 19.895 distance: 149 - 150: 32.724 distance: 149 - 158: 20.727 distance: 150 - 177: 31.138 distance: 151 - 152: 29.256 distance: 152 - 153: 21.379 distance: 152 - 154: 29.200 distance: 153 - 155: 31.262 distance: 154 - 156: 48.609 distance: 155 - 157: 11.668 distance: 156 - 157: 10.691