Starting phenix.real_space_refine on Mon Sep 30 13:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vhj_31996/09_2024/7vhj_31996.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 114 5.16 5 C 16167 2.51 5 N 4220 2.21 5 O 4852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25353 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 8485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1091, 8485 Classifications: {'peptide': 1091} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 54, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 8457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1087, 8457 Classifications: {'peptide': 1087} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 53, 'TRANS': 1033} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8411 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 16.14, per 1000 atoms: 0.64 Number of scatterers: 25353 At special positions: 0 Unit cell: (154.96, 160.16, 192.4, 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 114 16.00 O 4852 8.00 N 4220 7.00 C 16167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Time building additional restraints: 6.76 Conformation dependent library (CDL) restraints added in 3.5 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 48 sheets defined 22.6% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.138A 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 730 through 736 removed outlier: 3.813A pdb=" N TYR B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE B 735 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 748 removed outlier: 3.760A pdb=" N ASN B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.740A pdb=" N ASN B 757 " --> pdb=" O CYS B 753 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 819 removed outlier: 3.506A pdb=" N LEU B 814 " --> pdb=" O PHE B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 847 removed outlier: 3.842A pdb=" N LYS B 847 " --> pdb=" O ILE B 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 843 through 847' Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 859 through 876 Processing helix chain 'B' and resid 890 through 903 Processing helix chain 'B' and resid 906 through 912 removed outlier: 3.816A pdb=" N TYR B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 934 removed outlier: 4.289A pdb=" N THR B 934 " --> pdb=" O SER B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 958 Processing helix chain 'B' and resid 959 through 961 No H-bonds generated for 'chain 'B' and resid 959 through 961' Processing helix chain 'B' and resid 969 through 977 Processing helix chain 'B' and resid 978 through 1026 removed outlier: 4.983A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 1133 through 1140 removed outlier: 4.273A pdb=" N GLU B1137 " --> pdb=" O PRO B1133 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.917A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.006A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.638A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.259A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 736 Processing helix chain 'A' and resid 739 through 748 Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.898A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 819 removed outlier: 4.089A pdb=" N LEU A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.648A pdb=" N PHE A 848 " --> pdb=" O CYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 877 Processing helix chain 'A' and resid 879 through 884 Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.184A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 removed outlier: 3.958A pdb=" N THR A 934 " --> pdb=" O SER A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 removed outlier: 4.145A pdb=" N GLN A 942 " --> pdb=" O LEU A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 961 No H-bonds generated for 'chain 'A' and resid 959 through 961' Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.868A pdb=" N SER A 975 " --> pdb=" O ASN A 971 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG A 976 " --> pdb=" O ASP A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 1025 removed outlier: 3.613A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1113 Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.717A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.613A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 739 through 750 removed outlier: 3.643A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 776 Processing helix chain 'C' and resid 809 through 817 removed outlier: 3.956A pdb=" N ASN C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 877 Processing helix chain 'C' and resid 890 through 903 Processing helix chain 'C' and resid 905 through 934 removed outlier: 4.309A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS C 914 " --> pdb=" O TYR C 910 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU C 915 " --> pdb=" O GLU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 958 removed outlier: 4.063A pdb=" N GLN C 942 " --> pdb=" O LEU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 969 through 977 removed outlier: 3.529A pdb=" N ILE C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 976 " --> pdb=" O ASP C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.704A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1111 No H-bonds generated for 'chain 'C' and resid 1109 through 1111' Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.942A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 55 removed outlier: 4.104A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 158 removed outlier: 6.477A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 317 removed outlier: 5.320A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.478A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.575A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.741A pdb=" N VAL B 656 " --> pdb=" O ALA B 687 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR B 689 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN B 658 " --> pdb=" O THR B 689 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 704 through 708 Processing sheet with id=AB2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.611A pdb=" N MET B1043 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N TYR B1060 " --> pdb=" O HIS B1041 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N HIS B1041 " --> pdb=" O TYR B1060 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 716 through 720 Processing sheet with id=AB4, first strand: chain 'B' and resid 781 through 783 removed outlier: 5.791A pdb=" N ILE B 781 " --> pdb=" O ASN A 696 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1113 through 1116 removed outlier: 4.017A pdb=" N CYS B1075 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.543A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.735A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'A' and resid 101 through 103 removed outlier: 6.590A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.671A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 142 through 145 removed outlier: 5.823A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 314 through 317 removed outlier: 6.418A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 595 " --> pdb=" O SER A 316 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.713A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AC8, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AC9, first strand: chain 'A' and resid 551 through 553 removed outlier: 5.623A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.715A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A1043 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 704 through 720 removed outlier: 3.525A pdb=" N ILE A 707 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A1066 " --> pdb=" O ILE A 707 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A1064 " --> pdb=" O THR A 709 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE A 711 " --> pdb=" O PRO A1062 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 713 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A1060 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL A 715 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL A1058 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 717 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU A1056 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE A 719 " --> pdb=" O VAL A1054 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL A1054 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A1088 " --> pdb=" O ALA A1071 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 727 through 729 removed outlier: 3.828A pdb=" N SER A 728 " --> pdb=" O THR A 852 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1080 through 1081 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 5.078A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 53 removed outlier: 3.560A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 145 removed outlier: 6.640A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.768A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 313 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL C 597 " --> pdb=" O TYR C 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 327 removed outlier: 5.888A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AE4, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AE7, first strand: chain 'C' and resid 655 through 656 removed outlier: 8.040A pdb=" N VAL C 656 " --> pdb=" O ILE C 685 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA C 687 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 704 through 713 removed outlier: 6.919A pdb=" N SER C 704 " --> pdb=" O THR C1069 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C1069 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 706 " --> pdb=" O ASN C1067 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN C1067 " --> pdb=" O ALA C 706 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU C1065 " --> pdb=" O PRO C 708 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY C1052 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C1048 " --> pdb=" O GLY C1052 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL C1054 " --> pdb=" O PRO C1046 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU C1056 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER C1044 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C1040 " --> pdb=" O TYR C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AF2, first strand: chain 'C' and resid 1082 through 1083 Processing sheet with id=AF3, first strand: chain 'C' and resid 1087 through 1089 868 hydrogen bonds defined for protein. 2403 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: 11.71 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8217 1.34 - 1.46: 6265 1.46 - 1.58: 11324 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25950 Sorted by residual: bond pdb=" C ALA C1071 " pdb=" N PRO C1072 " ideal model delta sigma weight residual 1.337 1.323 0.014 9.80e-03 1.04e+04 2.02e+00 bond pdb=" C THR A 588 " pdb=" O THR A 588 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.86e+00 bond pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 1.808 1.765 0.043 3.30e-02 9.18e+02 1.71e+00 bond pdb=" C ASP C1132 " pdb=" N PRO C1133 " ideal model delta sigma weight residual 1.336 1.323 0.013 9.80e-03 1.04e+04 1.70e+00 bond pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.56e+00 ... (remaining 25945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 34359 1.62 - 3.25: 845 3.25 - 4.87: 104 4.87 - 6.49: 31 6.49 - 8.12: 7 Bond angle restraints: 35346 Sorted by residual: angle pdb=" C ILE A 587 " pdb=" N THR A 588 " pdb=" CA THR A 588 " ideal model delta sigma weight residual 122.64 118.86 3.78 1.25e+00 6.40e-01 9.15e+00 angle pdb=" N GLN A 173 " pdb=" CA GLN A 173 " pdb=" C GLN A 173 " ideal model delta sigma weight residual 108.97 114.12 -5.15 1.82e+00 3.02e-01 7.99e+00 angle pdb=" N PRO C 979 " pdb=" CA PRO C 979 " pdb=" C PRO C 979 " ideal model delta sigma weight residual 110.70 113.91 -3.21 1.22e+00 6.72e-01 6.91e+00 angle pdb=" C LYS C 847 " pdb=" N PHE C 848 " pdb=" CA PHE C 848 " ideal model delta sigma weight residual 121.54 126.56 -5.02 1.91e+00 2.74e-01 6.90e+00 angle pdb=" CA TRP B 64 " pdb=" CB TRP B 64 " pdb=" CG TRP B 64 " ideal model delta sigma weight residual 113.60 118.49 -4.89 1.90e+00 2.77e-01 6.62e+00 ... (remaining 35341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 14004 17.59 - 35.18: 1220 35.18 - 52.77: 163 52.77 - 70.35: 35 70.35 - 87.94: 20 Dihedral angle restraints: 15442 sinusoidal: 5961 harmonic: 9481 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 1.29 -87.29 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 731 " pdb=" SG CYS A 731 " pdb=" SG CYS A 753 " pdb=" CB CYS A 753 " ideal model delta sinusoidal sigma weight residual -86.00 -6.80 -79.20 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.34 -77.66 1 1.00e+01 1.00e-02 7.55e+01 ... (remaining 15439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2871 0.042 - 0.084: 838 0.084 - 0.126: 279 0.126 - 0.168: 18 0.168 - 0.210: 2 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CA CYS A 617 " pdb=" N CYS A 617 " pdb=" C CYS A 617 " pdb=" CB CYS A 617 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE C 101 " pdb=" CA ILE C 101 " pdb=" CG1 ILE C 101 " pdb=" CG2 ILE C 101 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" CB ILE C 410 " pdb=" CA ILE C 410 " pdb=" CG1 ILE C 410 " pdb=" CG2 ILE C 410 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.68e-01 ... (remaining 4005 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO C 561 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 174 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 520 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO B 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 585 2.67 - 3.23: 26054 3.23 - 3.78: 39097 3.78 - 4.34: 52634 4.34 - 4.90: 84240 Nonbonded interactions: 202610 Sorted by model distance: nonbonded pdb=" O LEU A 959 " pdb=" OG SER A 968 " model vdw 2.109 3.040 nonbonded pdb=" OH TYR C 749 " pdb=" OD1 ASP C 987 " model vdw 2.120 3.040 nonbonded pdb=" OG1 THR B 376 " pdb=" O ALA B 435 " model vdw 2.125 3.040 nonbonded pdb=" O VAL B1033 " pdb=" OG SER C1023 " model vdw 2.154 3.040 nonbonded pdb=" NH1 ARG B 898 " pdb=" O LEU B1042 " model vdw 2.155 3.120 ... (remaining 202605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 465 or (resid 466 and (name N o \ r name CA or name C or name O or name CB )) or resid 467 through 527 or (resid 5 \ 28 through 529 and (name N or name CA or name C or name O or name CB )) or resid \ 530 through 553 or (resid 554 and (name N or name CA or name C or name O or nam \ e CB )) or resid 555 through 582 or (resid 583 and (name N or name CA or name C \ or name O or name CB )) or resid 584 through 621 or resid 640 through 645 or (re \ sid 646 through 647 and (name N or name CA or name C or name O or name CB )) or \ resid 648 through 820 or resid 845 through 1140)) selection = (chain 'B' and (resid 27 through 416 or (resid 417 and (name N or name CA or nam \ e C or name O or name CB )) or resid 418 through 423 or (resid 424 and (name N o \ r name CA or name C or name O or name CB )) or resid 425 through 453 or (resid 4 \ 54 and (name N or name CA or name C or name O or name CB )) or resid 455 through \ 456 or (resid 457 and (name N or name CA or name C or name O or name CB )) or r \ esid 458 through 465 or (resid 466 and (name N or name CA or name C or name O or \ name CB )) or resid 467 through 621 or resid 640 through 645 or (resid 646 thro \ ugh 647 and (name N or name CA or name C or name O or name CB )) or resid 648 th \ rough 820 or resid 845 through 1140)) selection = (chain 'C' and (resid 27 through 332 or (resid 333 and (name N or name CA or nam \ e C or name O or name CB )) or resid 334 through 416 or (resid 417 and (name N o \ r name CA or name C or name O or name CB )) or resid 418 through 423 or (resid 4 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 425 through \ 453 or (resid 454 and (name N or name CA or name C or name O or name CB )) or r \ esid 455 through 456 or (resid 457 and (name N or name CA or name C or name O or \ name CB )) or resid 458 through 527 or (resid 528 through 529 and (name N or na \ me CA or name C or name O or name CB )) or resid 530 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 582 \ or (resid 583 and (name N or name CA or name C or name O or name CB )) or resid \ 584 through 621 or resid 640 through 1099 or (resid 1100 and (name N or name CA \ or name C or name O or name CB )) or resid 1101 through 1140)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 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: 0.000 Extract box with map and model: 0.920 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 61.700 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.170 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: 0.020 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 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 : 0.004 0.047 25950 Z= 0.260 Angle : 0.646 8.118 35346 Z= 0.359 Chirality : 0.044 0.210 4008 Planarity : 0.004 0.043 4596 Dihedral : 13.111 87.943 9235 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % 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: -3.85 (0.12), residues: 3239 helix: -1.73 (0.17), residues: 667 sheet: -2.15 (0.19), residues: 634 loop : -3.15 (0.12), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 633 HIS 0.011 0.001 HIS B1041 PHE 0.025 0.002 PHE C 899 TYR 0.019 0.002 TYR B 351 ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 342 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 122 ASN cc_start: 0.6300 (p0) cc_final: 0.5142 (m-40) REVERT: B 135 PHE cc_start: 0.7154 (m-10) cc_final: 0.6279 (m-80) REVERT: B 153 MET cc_start: 0.7837 (mtt) cc_final: 0.6955 (tpp) REVERT: B 374 PHE cc_start: 0.6647 (m-10) cc_final: 0.6368 (m-10) REVERT: B 392 PHE cc_start: 0.3311 (p90) cc_final: 0.3061 (p90) REVERT: B 408 ARG cc_start: 0.8176 (ptt90) cc_final: 0.7956 (ptt-90) REVERT: B 862 MET cc_start: 0.8306 (ptp) cc_final: 0.7832 (ptp) REVERT: B 958 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8400 (tt0) REVERT: B 986 ILE cc_start: 0.9296 (mm) cc_final: 0.9009 (mt) REVERT: A 30 ASN cc_start: 0.7892 (t0) cc_final: 0.7499 (m110) REVERT: A 190 ARG cc_start: 0.5731 (mtt180) cc_final: 0.5524 (mtt180) REVERT: A 195 LYS cc_start: 0.8524 (pttt) cc_final: 0.8278 (pttt) REVERT: A 449 TYR cc_start: 0.5651 (m-80) cc_final: 0.5070 (m-10) REVERT: A 516 GLU cc_start: 0.7436 (pm20) cc_final: 0.6680 (pm20) REVERT: A 569 ILE cc_start: 0.8104 (tt) cc_final: 0.7656 (tp) REVERT: A 733 MET cc_start: 0.8651 (tpp) cc_final: 0.8195 (tpt) REVERT: A 767 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8431 (mt0) REVERT: A 881 PHE cc_start: 0.8160 (p90) cc_final: 0.7884 (p90) REVERT: C 129 LYS cc_start: 0.8656 (pttp) cc_final: 0.8377 (pttp) REVERT: C 141 LEU cc_start: 0.8069 (tp) cc_final: 0.7848 (tp) REVERT: C 402 ILE cc_start: 0.8729 (mm) cc_final: 0.8521 (mm) REVERT: C 995 GLN cc_start: 0.8033 (tt0) cc_final: 0.7821 (tp40) outliers start: 2 outliers final: 1 residues processed: 344 average time/residue: 0.4178 time to fit residues: 225.3499 Evaluate side-chains 179 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 178 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 7.9990 chunk 245 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 154 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 chunk 294 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 69 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 245 HIS B 271 GLN B 394 ASN B 474 GLN B 865 GLN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 ASN B1135 GLN A 49 HIS A 66 HIS A 125 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 188 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 282 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 121 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN C 314 GLN C 414 GLN C 544 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS C1064 GLN C1076 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25950 Z= 0.257 Angle : 0.625 8.588 35346 Z= 0.332 Chirality : 0.044 0.185 4008 Planarity : 0.004 0.044 4596 Dihedral : 5.323 24.023 3493 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.19 % 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: -2.82 (0.13), residues: 3239 helix: -0.28 (0.19), residues: 669 sheet: -1.71 (0.19), residues: 638 loop : -2.64 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 64 HIS 0.008 0.001 HIS C 66 PHE 0.021 0.002 PHE C 157 TYR 0.021 0.002 TYR B 266 ARG 0.006 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 293 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7707 (mtt) cc_final: 0.6760 (tpp) REVERT: B 582 LEU cc_start: 0.8278 (mt) cc_final: 0.7832 (pp) REVERT: B 958 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8077 (tp-100) REVERT: B 986 ILE cc_start: 0.9346 (mm) cc_final: 0.9052 (mt) REVERT: A 30 ASN cc_start: 0.7881 (t0) cc_final: 0.7680 (m110) REVERT: A 195 LYS cc_start: 0.8581 (pttt) cc_final: 0.8331 (pttt) REVERT: A 242 LEU cc_start: 0.8205 (mt) cc_final: 0.8004 (mt) REVERT: A 449 TYR cc_start: 0.5763 (m-80) cc_final: 0.5017 (m-10) REVERT: A 451 TYR cc_start: 0.6151 (m-80) cc_final: 0.5873 (m-80) REVERT: A 733 MET cc_start: 0.8558 (tpp) cc_final: 0.8263 (tpt) REVERT: A 807 LYS cc_start: 0.7869 (mmtt) cc_final: 0.6854 (mmmt) REVERT: C 129 LYS cc_start: 0.8625 (pttp) cc_final: 0.8374 (pttp) REVERT: C 153 MET cc_start: 0.7073 (mmm) cc_final: 0.6868 (mmm) REVERT: C 402 ILE cc_start: 0.8748 (mm) cc_final: 0.8470 (mm) REVERT: C 514 SER cc_start: 0.8294 (t) cc_final: 0.8080 (m) outliers start: 3 outliers final: 0 residues processed: 296 average time/residue: 0.3450 time to fit residues: 166.5062 Evaluate side-chains 170 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.0270 chunk 91 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 overall best weight: 1.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 921 ASN ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN A 894 GLN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 958 GLN ** C 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25950 Z= 0.229 Angle : 0.600 8.167 35346 Z= 0.317 Chirality : 0.044 0.173 4008 Planarity : 0.004 0.044 4596 Dihedral : 5.164 25.549 3493 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3239 helix: 0.40 (0.20), residues: 665 sheet: -1.36 (0.20), residues: 633 loop : -2.35 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.013 0.001 HIS A 66 PHE 0.039 0.002 PHE B 816 TYR 0.018 0.001 TYR A 453 ARG 0.009 0.001 ARG A 988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7637 (mtt) cc_final: 0.6714 (tpp) REVERT: B 237 ARG cc_start: 0.6726 (mtm180) cc_final: 0.6499 (mtm-85) REVERT: B 374 PHE cc_start: 0.6640 (m-10) cc_final: 0.6416 (m-10) REVERT: B 392 PHE cc_start: 0.3537 (p90) cc_final: 0.2860 (p90) REVERT: B 425 LEU cc_start: 0.6409 (mt) cc_final: 0.5808 (tp) REVERT: B 958 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8012 (tp-100) REVERT: B 986 ILE cc_start: 0.9369 (mm) cc_final: 0.9051 (mt) REVERT: A 195 LYS cc_start: 0.8567 (pttt) cc_final: 0.8355 (pttt) REVERT: A 394 ASN cc_start: 0.8280 (m110) cc_final: 0.7647 (m-40) REVERT: A 449 TYR cc_start: 0.5781 (m-80) cc_final: 0.4994 (m-10) REVERT: A 516 GLU cc_start: 0.7190 (pm20) cc_final: 0.6552 (pm20) REVERT: A 733 MET cc_start: 0.8520 (tpp) cc_final: 0.8282 (tpt) REVERT: A 807 LYS cc_start: 0.7888 (mmtt) cc_final: 0.6876 (mmmt) REVERT: C 129 LYS cc_start: 0.8694 (pttp) cc_final: 0.8443 (pttp) REVERT: C 402 ILE cc_start: 0.8685 (mm) cc_final: 0.8402 (mm) REVERT: C 571 ASP cc_start: 0.7222 (t70) cc_final: 0.6897 (t0) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3524 time to fit residues: 159.1952 Evaluate side-chains 171 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 152 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 295 optimal weight: 9.9990 chunk 313 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 998 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 25950 Z= 0.281 Angle : 0.613 9.715 35346 Z= 0.323 Chirality : 0.044 0.174 4008 Planarity : 0.004 0.074 4596 Dihedral : 5.178 24.394 3493 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -2.09 (0.14), residues: 3239 helix: 0.61 (0.20), residues: 663 sheet: -1.30 (0.20), residues: 643 loop : -2.26 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.009 0.001 HIS A 66 PHE 0.025 0.002 PHE C 92 TYR 0.015 0.002 TYR B 866 ARG 0.005 0.000 ARG C 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7675 (mtt) cc_final: 0.6741 (tpp) REVERT: B 237 ARG cc_start: 0.6849 (mtm180) cc_final: 0.6587 (mtm-85) REVERT: B 425 LEU cc_start: 0.6610 (mt) cc_final: 0.6195 (tp) REVERT: B 958 GLN cc_start: 0.8633 (mm-40) cc_final: 0.7999 (tp-100) REVERT: B 986 ILE cc_start: 0.9341 (mm) cc_final: 0.8991 (mt) REVERT: A 177 MET cc_start: 0.6204 (mmm) cc_final: 0.5960 (mmm) REVERT: A 195 LYS cc_start: 0.8559 (pttt) cc_final: 0.7625 (ptmt) REVERT: A 394 ASN cc_start: 0.8296 (m110) cc_final: 0.8080 (m110) REVERT: A 449 TYR cc_start: 0.5874 (m-80) cc_final: 0.5043 (m-10) REVERT: A 516 GLU cc_start: 0.7445 (pm20) cc_final: 0.7103 (pm20) REVERT: A 807 LYS cc_start: 0.7882 (mmtt) cc_final: 0.6883 (mmmt) REVERT: C 129 LYS cc_start: 0.8678 (pttp) cc_final: 0.8442 (pttp) REVERT: C 402 ILE cc_start: 0.8666 (mm) cc_final: 0.8438 (mm) REVERT: C 571 ASP cc_start: 0.7276 (t70) cc_final: 0.6927 (t0) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3258 time to fit residues: 140.6055 Evaluate side-chains 160 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 216 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 281 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25950 Z= 0.305 Angle : 0.631 9.039 35346 Z= 0.333 Chirality : 0.045 0.224 4008 Planarity : 0.004 0.073 4596 Dihedral : 5.256 24.483 3493 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.04 % Allowed : 3.68 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3239 helix: 0.61 (0.20), residues: 665 sheet: -1.22 (0.20), residues: 638 loop : -2.21 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 104 HIS 0.008 0.001 HIS A 66 PHE 0.028 0.002 PHE B 374 TYR 0.020 0.002 TYR C 897 ARG 0.008 0.001 ARG B 808 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 244 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7761 (mtt) cc_final: 0.6817 (tpp) REVERT: B 237 ARG cc_start: 0.6894 (mtm180) cc_final: 0.6637 (mtm-85) REVERT: B 425 LEU cc_start: 0.6847 (mt) cc_final: 0.6055 (mp) REVERT: B 958 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8029 (tp-100) REVERT: B 986 ILE cc_start: 0.9345 (mm) cc_final: 0.9074 (mt) REVERT: A 195 LYS cc_start: 0.8551 (pttt) cc_final: 0.7623 (ptmt) REVERT: A 807 LYS cc_start: 0.7841 (mmtt) cc_final: 0.6781 (mmmt) REVERT: A 895 MET cc_start: 0.8394 (mmp) cc_final: 0.7973 (mmp) REVERT: C 129 LYS cc_start: 0.8710 (pttp) cc_final: 0.8455 (pttp) REVERT: C 402 ILE cc_start: 0.8653 (mm) cc_final: 0.8386 (mm) REVERT: C 571 ASP cc_start: 0.7359 (t70) cc_final: 0.6955 (t0) REVERT: C 754 THR cc_start: 0.8176 (p) cc_final: 0.7821 (t) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.3393 time to fit residues: 138.0094 Evaluate side-chains 153 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 2.9990 chunk 282 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 313 optimal weight: 2.9990 chunk 260 optimal weight: 0.3980 chunk 145 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 GLN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25950 Z= 0.193 Angle : 0.578 8.653 35346 Z= 0.304 Chirality : 0.043 0.202 4008 Planarity : 0.004 0.055 4596 Dihedral : 4.998 24.892 3493 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -1.74 (0.15), residues: 3239 helix: 0.92 (0.20), residues: 672 sheet: -1.12 (0.20), residues: 687 loop : -2.04 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 436 HIS 0.008 0.001 HIS A 66 PHE 0.025 0.001 PHE B 374 TYR 0.014 0.001 TYR C 265 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7348 (mtt) cc_final: 0.6940 (tpp) REVERT: B 237 ARG cc_start: 0.6954 (mtm180) cc_final: 0.6699 (mtm-85) REVERT: B 374 PHE cc_start: 0.6692 (m-10) cc_final: 0.6234 (m-10) REVERT: B 425 LEU cc_start: 0.6757 (mt) cc_final: 0.6270 (mp) REVERT: B 986 ILE cc_start: 0.9316 (mm) cc_final: 0.8919 (mt) REVERT: A 177 MET cc_start: 0.5525 (mmm) cc_final: 0.5128 (mmm) REVERT: A 195 LYS cc_start: 0.8427 (pttt) cc_final: 0.7986 (pttm) REVERT: A 233 ILE cc_start: 0.7588 (tt) cc_final: 0.7009 (mt) REVERT: A 449 TYR cc_start: 0.5787 (m-80) cc_final: 0.4859 (m-10) REVERT: A 807 LYS cc_start: 0.7751 (mmtt) cc_final: 0.6741 (mmmt) REVERT: A 895 MET cc_start: 0.8369 (mmp) cc_final: 0.8127 (mmp) REVERT: A 966 ILE cc_start: 0.8128 (mm) cc_final: 0.7924 (mm) REVERT: C 402 ILE cc_start: 0.8684 (mm) cc_final: 0.8301 (mm) REVERT: C 571 ASP cc_start: 0.7326 (t70) cc_final: 0.6939 (t0) REVERT: C 754 THR cc_start: 0.8087 (p) cc_final: 0.7680 (t) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.3195 time to fit residues: 141.7001 Evaluate side-chains 167 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 25950 Z= 0.327 Angle : 0.647 8.791 35346 Z= 0.340 Chirality : 0.045 0.191 4008 Planarity : 0.005 0.068 4596 Dihedral : 5.240 26.766 3493 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 0.04 % Allowed : 1.66 % Favored : 98.30 % 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: -1.86 (0.14), residues: 3239 helix: 0.78 (0.20), residues: 665 sheet: -1.16 (0.20), residues: 662 loop : -2.10 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 104 HIS 0.008 0.001 HIS A 66 PHE 0.035 0.002 PHE C 392 TYR 0.018 0.002 TYR C 749 ARG 0.005 0.001 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 240 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7456 (mtt) cc_final: 0.6953 (tpp) REVERT: B 374 PHE cc_start: 0.6720 (m-10) cc_final: 0.6263 (m-10) REVERT: B 425 LEU cc_start: 0.6929 (mt) cc_final: 0.6191 (mp) REVERT: A 177 MET cc_start: 0.5675 (mmm) cc_final: 0.5447 (mmm) REVERT: A 195 LYS cc_start: 0.8576 (pttt) cc_final: 0.7431 (pttt) REVERT: A 242 LEU cc_start: 0.8139 (mt) cc_final: 0.7931 (mt) REVERT: A 724 MET cc_start: 0.8455 (ptm) cc_final: 0.8072 (ptm) REVERT: A 807 LYS cc_start: 0.7849 (mmtt) cc_final: 0.6809 (mmmt) REVERT: A 895 MET cc_start: 0.8697 (mmp) cc_final: 0.8341 (mmp) REVERT: C 402 ILE cc_start: 0.8680 (mm) cc_final: 0.8327 (mm) REVERT: C 571 ASP cc_start: 0.7341 (t70) cc_final: 0.6982 (t0) REVERT: C 1022 MET cc_start: 0.8826 (tpp) cc_final: 0.8600 (tpp) REVERT: C 1043 MET cc_start: 0.8474 (ptp) cc_final: 0.8078 (ptp) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.3311 time to fit residues: 134.9381 Evaluate side-chains 157 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 212 optimal weight: 0.0980 chunk 154 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 564 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25950 Z= 0.194 Angle : 0.582 8.870 35346 Z= 0.307 Chirality : 0.044 0.213 4008 Planarity : 0.004 0.061 4596 Dihedral : 4.981 27.629 3493 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -1.70 (0.14), residues: 3239 helix: 0.97 (0.20), residues: 667 sheet: -1.05 (0.20), residues: 675 loop : -2.03 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.018 0.001 HIS B1041 PHE 0.036 0.001 PHE A 275 TYR 0.016 0.001 TYR C 508 ARG 0.016 0.000 ARG B1012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7549 (mtt) cc_final: 0.6933 (tpp) REVERT: B 425 LEU cc_start: 0.6757 (mt) cc_final: 0.6385 (tp) REVERT: A 177 MET cc_start: 0.5697 (mmm) cc_final: 0.5424 (mmm) REVERT: A 195 LYS cc_start: 0.8559 (pttt) cc_final: 0.8347 (pttt) REVERT: A 233 ILE cc_start: 0.7599 (tt) cc_final: 0.7004 (mt) REVERT: A 449 TYR cc_start: 0.5862 (m-80) cc_final: 0.4939 (m-10) REVERT: A 807 LYS cc_start: 0.7786 (mmtt) cc_final: 0.6757 (mmmt) REVERT: A 895 MET cc_start: 0.8337 (mmp) cc_final: 0.8042 (mmp) REVERT: C 402 ILE cc_start: 0.8698 (mm) cc_final: 0.8405 (mm) REVERT: C 571 ASP cc_start: 0.7352 (t70) cc_final: 0.6942 (t0) REVERT: C 1043 MET cc_start: 0.8414 (ptp) cc_final: 0.8040 (ptp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.3216 time to fit residues: 146.0115 Evaluate side-chains 166 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.4980 chunk 299 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 291 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 262 optimal weight: 0.0000 chunk 275 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 overall best weight: 1.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 894 GLN ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25950 Z= 0.229 Angle : 0.599 8.656 35346 Z= 0.315 Chirality : 0.044 0.201 4008 Planarity : 0.004 0.057 4596 Dihedral : 4.974 26.115 3493 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.64 (0.15), residues: 3239 helix: 0.97 (0.21), residues: 668 sheet: -1.00 (0.20), residues: 658 loop : -1.97 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.012 0.001 HIS C 66 PHE 0.036 0.001 PHE A 275 TYR 0.018 0.001 TYR B 866 ARG 0.007 0.000 ARG A1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7543 (mtt) cc_final: 0.6911 (tpp) REVERT: B 425 LEU cc_start: 0.6753 (mt) cc_final: 0.6440 (tp) REVERT: A 195 LYS cc_start: 0.8620 (pttt) cc_final: 0.8372 (pttt) REVERT: A 807 LYS cc_start: 0.7742 (mmtt) cc_final: 0.6739 (mmmt) REVERT: A 888 GLN cc_start: 0.8385 (mp10) cc_final: 0.8053 (mp10) REVERT: A 895 MET cc_start: 0.8487 (mmp) cc_final: 0.8194 (mmp) REVERT: C 402 ILE cc_start: 0.8663 (mm) cc_final: 0.8382 (mm) REVERT: C 571 ASP cc_start: 0.7371 (t70) cc_final: 0.6996 (t0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.3359 time to fit residues: 144.3575 Evaluate side-chains 164 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.6980 chunk 307 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1057 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25950 Z= 0.283 Angle : 0.629 8.581 35346 Z= 0.333 Chirality : 0.044 0.214 4008 Planarity : 0.004 0.053 4596 Dihedral : 5.108 25.211 3493 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.70 (0.14), residues: 3239 helix: 0.81 (0.20), residues: 673 sheet: -1.01 (0.20), residues: 644 loop : -1.98 (0.13), residues: 1922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.019 0.002 HIS B1041 PHE 0.032 0.002 PHE A 275 TYR 0.027 0.002 TYR B 866 ARG 0.006 0.000 ARG A1012 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.7602 (mtt) cc_final: 0.6909 (tpp) REVERT: B 425 LEU cc_start: 0.6824 (mt) cc_final: 0.6417 (tp) REVERT: B 893 MET cc_start: 0.8272 (mmm) cc_final: 0.7986 (mmm) REVERT: A 177 MET cc_start: 0.5630 (mmm) cc_final: 0.5326 (tpp) REVERT: A 195 LYS cc_start: 0.8617 (pttt) cc_final: 0.8383 (pttt) REVERT: A 724 MET cc_start: 0.8367 (ptm) cc_final: 0.8004 (ptm) REVERT: A 807 LYS cc_start: 0.7779 (mmtt) cc_final: 0.6730 (mmmt) REVERT: A 888 GLN cc_start: 0.8486 (mp10) cc_final: 0.8114 (mp10) REVERT: A 895 MET cc_start: 0.8555 (mmp) cc_final: 0.8216 (mmp) REVERT: A 961 SER cc_start: 0.9032 (t) cc_final: 0.8806 (p) REVERT: C 129 LYS cc_start: 0.8446 (pttm) cc_final: 0.8128 (pttp) REVERT: C 402 ILE cc_start: 0.8639 (mm) cc_final: 0.8348 (mm) REVERT: C 571 ASP cc_start: 0.7332 (t70) cc_final: 0.6935 (t0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.3471 time to fit residues: 145.5887 Evaluate side-chains 165 residues out of total 2839 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.6980 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 237 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 264 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 47 optimal weight: 0.0670 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 985 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 958 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.098603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077822 restraints weight = 86416.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078093 restraints weight = 66601.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078430 restraints weight = 49397.721| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25950 Z= 0.222 Angle : 0.597 9.094 35346 Z= 0.314 Chirality : 0.043 0.210 4008 Planarity : 0.004 0.054 4596 Dihedral : 4.967 24.797 3493 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -1.62 (0.15), residues: 3239 helix: 0.88 (0.20), residues: 677 sheet: -0.95 (0.20), residues: 658 loop : -1.94 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 436 HIS 0.018 0.001 HIS B1041 PHE 0.030 0.001 PHE C 157 TYR 0.019 0.001 TYR C 749 ARG 0.006 0.000 ARG A1012 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.86 seconds wall clock time: 84 minutes 23.67 seconds (5063.67 seconds total)