Starting phenix.real_space_refine on Mon Aug 25 09:28:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh9_40038/08_2025/8gh9_40038.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.009 sd= 0.063 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 178 5.16 5 C 17569 2.51 5 N 4401 2.21 5 O 4918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27066 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6644 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 830, 6636 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 804} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 830, 6636 Classifications: {'peptide': 830} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 804} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6779 Chain: "C" Number of atoms: 6900 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 866, 6892 Classifications: {'peptide': 866} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 838} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 866, 6892 Classifications: {'peptide': 866} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 838} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7041 Chain: "B" Number of atoms: 6651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 831, 6643 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 805} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 831, 6643 Classifications: {'peptide': 831} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 805} Chain breaks: 6 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 6786 Chain: "D" Number of atoms: 6871 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 862, 6863 Classifications: {'peptide': 862} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 834} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 862, 6863 Classifications: {'peptide': 862} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 27, 'TRANS': 834} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 7010 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AASN A 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN A 826 " occ=0.45 residue: pdb=" N AASN C 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN C 826 " occ=0.41 residue: pdb=" N AASN B 826 " occ=0.55 ... (14 atoms not shown) pdb=" ND2BASN B 826 " occ=0.45 residue: pdb=" N AASN D 826 " occ=0.59 ... (14 atoms not shown) pdb=" ND2BASN D 826 " occ=0.41 Time building chain proxies: 9.68, per 1000 atoms: 0.36 Number of scatterers: 27066 At special positions: 0 Unit cell: (152.28, 150.12, 132.84, 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 178 16.00 O 4918 8.00 N 4401 7.00 C 17569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.93 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6450 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 20 sheets defined 50.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 4.386A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 109 through 128 Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.542A pdb=" N ASN A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 170 removed outlier: 4.206A pdb=" N ASP A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 Processing helix chain 'A' and resid 180 through 199 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 210 through 215 removed outlier: 4.222A pdb=" N LEU A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 229 through 260 removed outlier: 3.763A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 4.200A pdb=" N CYS A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 319 removed outlier: 4.331A pdb=" N PHE A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 313 " --> pdb=" O LEU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.704A pdb=" N ASP A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 394 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 416 through 419 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.933A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.677A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 500 removed outlier: 3.578A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.641A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ALA A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 510 " --> pdb=" O MET A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.029A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 699 through 704 removed outlier: 3.816A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 747 through 751 removed outlier: 3.751A pdb=" N LEU A 751 " --> pdb=" O TYR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 767 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 791 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.598A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 892 removed outlier: 3.503A pdb=" N LEU A 891 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 888 through 892' Processing helix chain 'A' and resid 902 through 906 removed outlier: 3.600A pdb=" N LEU A 905 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 913 removed outlier: 3.657A pdb=" N THR A 913 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 921 Processing helix chain 'A' and resid 922 through 930 removed outlier: 4.158A pdb=" N PHE A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 941 Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 996 through 1008 Processing helix chain 'C' and resid 21 through 26 removed outlier: 4.488A pdb=" N LEU C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.683A pdb=" N PHE C 34 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 121 through 134 removed outlier: 3.845A pdb=" N GLY C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE C 129 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 170 removed outlier: 4.225A pdb=" N TYR C 163 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 232 through 260 removed outlier: 4.011A pdb=" N GLY C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 4.221A pdb=" N TYR C 279 " --> pdb=" O TRP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.163A pdb=" N PHE C 306 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 415 Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.657A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 471 Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.542A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.328A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 562 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 733 through 739 removed outlier: 3.616A pdb=" N LEU C 737 " --> pdb=" O GLY C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 743 removed outlier: 4.024A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 747 through 751 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O TYR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 768 removed outlier: 4.396A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 766 " --> pdb=" O TYR C 762 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.648A pdb=" N VAL C 792 " --> pdb=" O ASP C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 797 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 884 through 891 removed outlier: 4.145A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 removed outlier: 3.669A pdb=" N LEU C 905 " --> pdb=" O GLU C 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 902 through 905' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 921 through 930 removed outlier: 4.311A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 942 Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 969 through 973 Processing helix chain 'C' and resid 985 through 991 removed outlier: 4.318A pdb=" N ASP C 989 " --> pdb=" O PRO C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'B' and resid 22 through 29 removed outlier: 3.536A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 109 through 134 removed outlier: 4.575A pdb=" N LEU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 170 removed outlier: 3.658A pdb=" N ASP B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 180 through 199 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 207 through 211 removed outlier: 4.163A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 260 removed outlier: 3.623A pdb=" N ILE B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 319 Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 415 Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 432 through 451 removed outlier: 4.042A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 471 Processing helix chain 'B' and resid 486 through 500 removed outlier: 4.374A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 500 " --> pdb=" O GLN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 510 removed outlier: 3.552A pdb=" N LEU B 510 " --> pdb=" O MET B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.997A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 558 removed outlier: 4.508A pdb=" N VAL B 553 " --> pdb=" O SER B 549 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 554 " --> pdb=" O PHE B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 3.605A pdb=" N ARG B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.841A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 767 Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 791 Processing helix chain 'B' and resid 804 through 808 removed outlier: 3.614A pdb=" N GLN B 807 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN B 808 " --> pdb=" O ALA B 805 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 804 through 808' Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.826A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.773A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 890 " --> pdb=" O ASN B 887 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 916 through 921 removed outlier: 3.620A pdb=" N VAL B 919 " --> pdb=" O ALA B 916 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 921 " --> pdb=" O SER B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 removed outlier: 4.173A pdb=" N PHE B 929 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 941 removed outlier: 3.886A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG B 938 " --> pdb=" O LEU B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 957 Processing helix chain 'B' and resid 996 through 1007 Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.556A pdb=" N ALA D 27 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 removed outlier: 3.992A pdb=" N THR D 32 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 122 through 136 removed outlier: 3.601A pdb=" N LEU D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 170 removed outlier: 4.017A pdb=" N ASN D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 163 " --> pdb=" O PHE D 159 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.827A pdb=" N GLU D 219 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 260 removed outlier: 3.970A pdb=" N SER D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE D 241 " --> pdb=" O ASN D 237 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 297 through 318 removed outlier: 4.591A pdb=" N ALA D 316 " --> pdb=" O LEU D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.044A pdb=" N ILE D 323 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY D 327 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 415 Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.705A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 464 No H-bonds generated for 'chain 'D' and resid 462 through 464' Processing helix chain 'D' and resid 465 through 471 removed outlier: 3.816A pdb=" N ASN D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 498 Processing helix chain 'D' and resid 502 through 509 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.257A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 562 Processing helix chain 'D' and resid 601 through 606 Processing helix chain 'D' and resid 607 through 609 No H-bonds generated for 'chain 'D' and resid 607 through 609' Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 733 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.981A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 747 through 751 removed outlier: 3.583A pdb=" N LEU D 751 " --> pdb=" O TYR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.701A pdb=" N VAL D 792 " --> pdb=" O ASP D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 884 through 891 removed outlier: 4.066A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 removed outlier: 3.613A pdb=" N LEU D 905 " --> pdb=" O GLU D 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 902 through 905' Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 921 through 930 removed outlier: 4.348A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 942 Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 969 through 974 removed outlier: 3.541A pdb=" N ARG D 972 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 991 removed outlier: 4.307A pdb=" N ASP D 989 " --> pdb=" O PRO D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 378 removed outlier: 7.442A pdb=" N LYS A 343 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL A 376 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 345 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU A 378 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 347 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 457 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 539 removed outlier: 3.871A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 778 removed outlier: 6.340A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1014 through 1017 Processing sheet with id=AA5, first strand: chain 'C' and resid 398 through 399 removed outlier: 7.252A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 459 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 538 removed outlier: 3.557A pdb=" N ILE C 598 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 567 through 569 Processing sheet with id=AA8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.344A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 757 " --> pdb=" O VAL C 721 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET C 799 " --> pdb=" O HIS C 718 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 879 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 976 through 979 removed outlier: 4.304A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.719A pdb=" N SER B 140 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 373 through 377 removed outlier: 7.723A pdb=" N LYS B 343 " --> pdb=" O GLU B 374 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N VAL B 376 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 345 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 457 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN B 459 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 535 through 539 removed outlier: 7.174A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 776 through 780 removed outlier: 5.963A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 975 through 976 Processing sheet with id=AB6, first strand: chain 'B' and resid 1014 through 1017 Processing sheet with id=AB7, first strand: chain 'D' and resid 375 through 376 removed outlier: 6.175A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 539 removed outlier: 3.809A pdb=" N GLY D 595 " --> pdb=" O GLU D 539 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.214A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 757 " --> pdb=" O VAL D 721 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS D 718 " --> pdb=" O MET D 799 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N VAL D 801 " --> pdb=" O HIS D 718 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 981 removed outlier: 4.056A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1057 hydrogen bonds defined for protein. 2956 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: 4.58 Time building geometry restraints manager: 2.56 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: 8534 1.34 - 1.46: 6783 1.46 - 1.58: 12103 1.58 - 1.70: 0 1.70 - 1.82: 268 Bond restraints: 27688 Sorted by residual: bond pdb=" N TYR A 130 " pdb=" CA TYR A 130 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.37e+00 bond pdb=" CB ASN B 806 " pdb=" CG ASN B 806 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.35e+00 bond pdb=" CB ASP D 726 " pdb=" CG ASP D 726 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" CB GLN B 807 " pdb=" CG GLN B 807 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00 bond pdb=" CB ASN B 795 " pdb=" CG ASN B 795 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 27683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 37213 3.11 - 6.21: 297 6.21 - 9.32: 42 9.32 - 12.42: 10 12.42 - 15.53: 5 Bond angle restraints: 37567 Sorted by residual: angle pdb=" C SER D 286 " pdb=" CA SER D 286 " pdb=" CB SER D 286 " ideal model delta sigma weight residual 116.63 110.65 5.98 1.16e+00 7.43e-01 2.65e+01 angle pdb=" CB MET D1009 " pdb=" CG MET D1009 " pdb=" SD MET D1009 " ideal model delta sigma weight residual 112.70 127.24 -14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" CA LEU C 161 " pdb=" CB LEU C 161 " pdb=" CG LEU C 161 " ideal model delta sigma weight residual 116.30 131.83 -15.53 3.50e+00 8.16e-02 1.97e+01 angle pdb=" CA LEU C 206 " pdb=" CB LEU C 206 " pdb=" CG LEU C 206 " ideal model delta sigma weight residual 116.30 131.70 -15.40 3.50e+00 8.16e-02 1.94e+01 angle pdb=" CB MET D 282 " pdb=" CG MET D 282 " pdb=" SD MET D 282 " ideal model delta sigma weight residual 112.70 124.92 -12.22 3.00e+00 1.11e-01 1.66e+01 ... (remaining 37562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 13834 17.94 - 35.88: 1892 35.88 - 53.81: 512 53.81 - 71.75: 61 71.75 - 89.69: 22 Dihedral angle restraints: 16321 sinusoidal: 6373 harmonic: 9948 Sorted by residual: dihedral pdb=" CA ASN C1008 " pdb=" C ASN C1008 " pdb=" N MET C1009 " pdb=" CA MET C1009 " ideal model delta harmonic sigma weight residual 180.00 -155.13 -24.87 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU A 321 " pdb=" C GLU A 321 " pdb=" N ILE A 322 " pdb=" CA ILE A 322 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA THR D 352 " pdb=" C THR D 352 " pdb=" N LEU D 353 " pdb=" CA LEU D 353 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 16318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3262 0.049 - 0.099: 824 0.099 - 0.148: 207 0.148 - 0.198: 8 0.198 - 0.247: 1 Chirality restraints: 4302 Sorted by residual: chirality pdb=" CB ILE D 456 " pdb=" CA ILE D 456 " pdb=" CG1 ILE D 456 " pdb=" CG2 ILE D 456 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA LEU C 161 " pdb=" N LEU C 161 " pdb=" C LEU C 161 " pdb=" CB LEU C 161 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 806 " pdb=" N ASN B 806 " pdb=" C ASN B 806 " pdb=" CB ASN B 806 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 4299 not shown) Planarity restraints: 4717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1055 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C PHE A1055 " 0.053 2.00e-02 2.50e+03 pdb=" O PHE A1055 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A1056 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " -0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO A 192 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 191 " 0.040 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO C 192 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 192 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 192 " 0.034 5.00e-02 4.00e+02 ... (remaining 4714 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1208 2.72 - 3.26: 28002 3.26 - 3.81: 43720 3.81 - 4.35: 49895 4.35 - 4.90: 83824 Nonbonded interactions: 206649 Sorted by model distance: nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR B 290 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR B 273 " pdb=" OE1 GLU B 276 " model vdw 2.207 3.040 nonbonded pdb=" O THR B 935 " pdb=" OG1 THR B 939 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU C 417 " pdb=" OH TYR C 450 " model vdw 2.248 3.040 ... (remaining 206644 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 19 through 33 or resid 97 through 368 or resid 371 through \ 825 or resid 827 through 1056)) selection = (chain 'B' and (resid 19 through 33 or resid 97 through 368 or resid 371 through \ 825 or resid 827 through 976 or resid 995 through 1056)) selection = (chain 'C' and (resid 19 through 33 or resid 97 through 368 or resid 371 through \ 570 or resid 591 through 825 or resid 827 through 958 or resid 964 through 976 \ or resid 995 through 1056)) selection = (chain 'D' and (resid 19 through 33 or resid 97 through 570 or resid 591 through \ 825 or resid 827 through 958 or resid 964 through 976 or resid 995 through 1056 \ )) } 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=0.41 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 27.280 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.049 27688 Z= 0.169 Angle : 0.751 15.526 37567 Z= 0.371 Chirality : 0.045 0.247 4302 Planarity : 0.005 0.064 4717 Dihedral : 17.392 89.691 9871 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.37 % Allowed : 35.22 % Favored : 64.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.14), residues: 3351 helix: -0.29 (0.13), residues: 1500 sheet: -1.36 (0.30), residues: 347 loop : -1.64 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 393 TYR 0.036 0.001 TYR D 145 PHE 0.035 0.002 PHE A 252 TRP 0.021 0.001 TRP B 246 HIS 0.011 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00381 (27688) covalent geometry : angle 0.75083 (37567) hydrogen bonds : bond 0.13213 ( 1057) hydrogen bonds : angle 5.96445 ( 2956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 346 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: C 159 PHE cc_start: 0.8947 (t80) cc_final: 0.8300 (t80) REVERT: B 303 PHE cc_start: 0.8890 (m-80) cc_final: 0.8668 (m-10) REVERT: D 145 TYR cc_start: 0.6989 (m-80) cc_final: 0.6773 (m-80) outliers start: 11 outliers final: 7 residues processed: 355 average time/residue: 0.1372 time to fit residues: 83.1629 Evaluate side-chains 344 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 337 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain B residue 736 ASN Chi-restraints excluded: chain B residue 817 ASP Chi-restraints excluded: chain B residue 1000 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 200 ASN A 222 GLN A 440 ASN A 462 GLN A 534 ASN A 749 HIS A 907 GLN A 967 GLN C 143 ASN C 231 ASN C 397 GLN C 449 ASN C 979 GLN B 440 ASN B 465 ASN B 468 HIS B 496 GLN B 509 ASN B 534 ASN B 745 ASN B 907 GLN D 225 ASN D 365 HIS D 397 GLN D 402 GLN D 449 ASN D 534 ASN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 979 GLN D1021 HIS ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.139562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100954 restraints weight = 134448.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101867 restraints weight = 58799.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103511 restraints weight = 42334.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103946 restraints weight = 34072.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105052 restraints weight = 29756.080| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27688 Z= 0.161 Angle : 0.628 11.640 37567 Z= 0.317 Chirality : 0.042 0.176 4302 Planarity : 0.004 0.061 4717 Dihedral : 4.698 50.707 3630 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.34 % Allowed : 32.14 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.14), residues: 3351 helix: -0.01 (0.14), residues: 1486 sheet: -1.46 (0.30), residues: 359 loop : -1.50 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 393 TYR 0.032 0.001 TYR B 279 PHE 0.019 0.001 PHE A 159 TRP 0.017 0.001 TRP B 246 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00368 (27688) covalent geometry : angle 0.62837 (37567) hydrogen bonds : bond 0.04108 ( 1057) hydrogen bonds : angle 5.38983 ( 2956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 349 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 742 ARG cc_start: 0.7266 (mmm160) cc_final: 0.6923 (mmt180) REVERT: C 154 MET cc_start: 0.2979 (mmt) cc_final: 0.2759 (mmp) REVERT: C 159 PHE cc_start: 0.8929 (t80) cc_final: 0.8278 (t80) REVERT: C 712 MET cc_start: 0.8571 (mmp) cc_final: 0.8346 (mmm) REVERT: C 1009 MET cc_start: 0.8059 (mmm) cc_final: 0.7650 (mmm) REVERT: B 304 MET cc_start: 0.8346 (tpt) cc_final: 0.8008 (tpp) REVERT: D 145 TYR cc_start: 0.7072 (m-80) cc_final: 0.6800 (m-10) REVERT: D 303 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8579 (t80) outliers start: 100 outliers final: 59 residues processed: 416 average time/residue: 0.1345 time to fit residues: 95.1170 Evaluate side-chains 392 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 332 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 937 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1053 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 131 PHE Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1053 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 205 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 18 optimal weight: 0.0020 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN C 979 GLN D 402 GLN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.139686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.100429 restraints weight = 130623.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.101791 restraints weight = 56271.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.103057 restraints weight = 40592.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103693 restraints weight = 33348.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104636 restraints weight = 29172.690| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27688 Z= 0.138 Angle : 0.606 11.845 37567 Z= 0.303 Chirality : 0.042 0.173 4302 Planarity : 0.004 0.059 4717 Dihedral : 4.629 56.665 3626 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.31 % Allowed : 32.44 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.15), residues: 3351 helix: 0.10 (0.14), residues: 1494 sheet: -1.41 (0.30), residues: 351 loop : -1.47 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 393 TYR 0.015 0.001 TYR D 401 PHE 0.030 0.001 PHE C 160 TRP 0.015 0.001 TRP C 176 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00317 (27688) covalent geometry : angle 0.60573 (37567) hydrogen bonds : bond 0.03817 ( 1057) hydrogen bonds : angle 5.23252 ( 2956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 341 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: A 354 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: A 564 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8267 (tt) REVERT: C 154 MET cc_start: 0.2660 (mmt) cc_final: 0.2388 (mmp) REVERT: C 159 PHE cc_start: 0.8905 (t80) cc_final: 0.8040 (m-80) REVERT: C 160 PHE cc_start: 0.8266 (m-80) cc_final: 0.7994 (m-80) REVERT: C 726 ASP cc_start: 0.8409 (p0) cc_final: 0.8127 (p0) REVERT: C 799 MET cc_start: 0.8037 (tpp) cc_final: 0.7632 (tpp) REVERT: C 982 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7402 (pp) REVERT: D 145 TYR cc_start: 0.6932 (m-80) cc_final: 0.6451 (m-10) REVERT: D 303 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8605 (t80) REVERT: D 307 PHE cc_start: 0.8613 (m-80) cc_final: 0.7495 (m-80) REVERT: D 1009 MET cc_start: 0.8349 (tpt) cc_final: 0.8068 (tpp) outliers start: 98 outliers final: 59 residues processed: 415 average time/residue: 0.1335 time to fit residues: 94.3968 Evaluate side-chains 392 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 328 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 925 SER Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1052 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 274 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 331 optimal weight: 0.0170 chunk 179 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 312 optimal weight: 6.9990 chunk 264 optimal weight: 4.9990 chunk 258 optimal weight: 0.2980 chunk 326 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 979 GLN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.141019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.101213 restraints weight = 140503.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103770 restraints weight = 57542.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105478 restraints weight = 37075.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105925 restraints weight = 30089.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.106731 restraints weight = 26856.606| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27688 Z= 0.102 Angle : 0.585 13.342 37567 Z= 0.290 Chirality : 0.041 0.195 4302 Planarity : 0.004 0.065 4717 Dihedral : 4.481 58.350 3626 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.31 % Allowed : 32.58 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.15), residues: 3351 helix: 0.24 (0.14), residues: 1488 sheet: -1.30 (0.29), residues: 359 loop : -1.46 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 742 TYR 0.009 0.001 TYR A 279 PHE 0.026 0.001 PHE C 160 TRP 0.015 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00219 (27688) covalent geometry : angle 0.58531 (37567) hydrogen bonds : bond 0.03396 ( 1057) hydrogen bonds : angle 5.04321 ( 2956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 363 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8203 (pm20) REVERT: C 159 PHE cc_start: 0.8850 (t80) cc_final: 0.7951 (m-80) REVERT: C 160 PHE cc_start: 0.8277 (m-80) cc_final: 0.7876 (m-80) REVERT: C 799 MET cc_start: 0.8126 (tpp) cc_final: 0.7679 (tpp) REVERT: C 982 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7161 (pp) REVERT: C 1009 MET cc_start: 0.8449 (mmm) cc_final: 0.7485 (mmm) REVERT: D 145 TYR cc_start: 0.6976 (m-80) cc_final: 0.6380 (m-80) REVERT: D 282 MET cc_start: 0.8931 (tpp) cc_final: 0.8643 (tpp) REVERT: D 303 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8571 (t80) REVERT: D 307 PHE cc_start: 0.8695 (m-80) cc_final: 0.7338 (m-80) REVERT: D 1009 MET cc_start: 0.8297 (tpt) cc_final: 0.7856 (mmm) outliers start: 98 outliers final: 58 residues processed: 437 average time/residue: 0.1401 time to fit residues: 103.8623 Evaluate side-chains 401 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 340 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 32 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 chunk 196 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 335 optimal weight: 5.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN C 142 GLN C 462 GLN D 402 GLN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 772 ASN ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094581 restraints weight = 137190.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.097064 restraints weight = 59189.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098353 restraints weight = 38945.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098909 restraints weight = 32633.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099577 restraints weight = 29300.653| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27688 Z= 0.220 Angle : 0.665 11.544 37567 Z= 0.335 Chirality : 0.044 0.158 4302 Planarity : 0.004 0.055 4717 Dihedral : 4.727 51.008 3625 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.58 % Allowed : 31.34 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.15), residues: 3351 helix: 0.06 (0.14), residues: 1496 sheet: -1.65 (0.29), residues: 351 loop : -1.47 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 393 TYR 0.019 0.001 TYR B1032 PHE 0.024 0.002 PHE B 131 TRP 0.020 0.001 TRP C 176 HIS 0.005 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00509 (27688) covalent geometry : angle 0.66526 (37567) hydrogen bonds : bond 0.04162 ( 1057) hydrogen bonds : angle 5.35629 ( 2956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 336 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8405 (pm20) REVERT: A 279 TYR cc_start: 0.8172 (m-80) cc_final: 0.7501 (m-80) REVERT: A 321 GLU cc_start: 0.8616 (pm20) cc_final: 0.8323 (pm20) REVERT: A 354 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: A 393 ARG cc_start: 0.8135 (ptp90) cc_final: 0.7888 (ptp90) REVERT: A 564 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8356 (tt) REVERT: C 159 PHE cc_start: 0.8891 (t80) cc_final: 0.8024 (m-80) REVERT: C 160 PHE cc_start: 0.8376 (m-80) cc_final: 0.8012 (m-80) REVERT: C 307 PHE cc_start: 0.8703 (m-80) cc_final: 0.8407 (m-80) REVERT: C 513 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6889 (tpp) REVERT: C 799 MET cc_start: 0.8283 (tpp) cc_final: 0.7848 (tpt) REVERT: C 982 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7493 (pp) REVERT: C 1009 MET cc_start: 0.8516 (mmm) cc_final: 0.7533 (mmm) REVERT: D 145 TYR cc_start: 0.7033 (m-80) cc_final: 0.6370 (m-80) REVERT: D 282 MET cc_start: 0.9013 (tpp) cc_final: 0.8745 (tpp) REVERT: D 303 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8617 (t80) REVERT: D 1009 MET cc_start: 0.8311 (tpt) cc_final: 0.7950 (mmm) outliers start: 136 outliers final: 90 residues processed: 436 average time/residue: 0.1377 time to fit residues: 101.6695 Evaluate side-chains 420 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 324 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 513 MET Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 942 THR Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 159 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 797 CYS Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 904 TYR Chi-restraints excluded: chain B residue 922 SER Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 242 PHE Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 402 GLN Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 982 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 156 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 263 optimal weight: 0.6980 chunk 267 optimal weight: 8.9990 chunk 336 optimal weight: 2.9990 chunk 139 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 170 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 211 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.141702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.101841 restraints weight = 125091.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103914 restraints weight = 54146.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105101 restraints weight = 35388.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.106603 restraints weight = 28781.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106681 restraints weight = 24966.313| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27688 Z= 0.106 Angle : 0.599 13.242 37567 Z= 0.295 Chirality : 0.042 0.186 4302 Planarity : 0.004 0.056 4717 Dihedral : 4.400 52.571 3622 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.94 % Allowed : 33.34 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.15), residues: 3351 helix: 0.24 (0.14), residues: 1487 sheet: -1.47 (0.29), residues: 361 loop : -1.45 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 393 TYR 0.025 0.001 TYR C 279 PHE 0.029 0.001 PHE B 131 TRP 0.016 0.001 TRP B 246 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00232 (27688) covalent geometry : angle 0.59865 (37567) hydrogen bonds : bond 0.03420 ( 1057) hydrogen bonds : angle 5.04907 ( 2956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 352 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8231 (pm20) REVERT: A 279 TYR cc_start: 0.8119 (m-80) cc_final: 0.7484 (m-80) REVERT: A 321 GLU cc_start: 0.8574 (pm20) cc_final: 0.8281 (pm20) REVERT: A 521 GLU cc_start: 0.8492 (mp0) cc_final: 0.8285 (pm20) REVERT: A 564 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (tt) REVERT: A 739 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8045 (tpt) REVERT: C 159 PHE cc_start: 0.8845 (t80) cc_final: 0.7952 (m-80) REVERT: C 160 PHE cc_start: 0.8298 (m-80) cc_final: 0.7955 (m-80) REVERT: C 303 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8444 (t80) REVERT: C 423 LEU cc_start: 0.8934 (mp) cc_final: 0.8706 (mp) REVERT: C 799 MET cc_start: 0.8220 (tpp) cc_final: 0.7791 (tpt) REVERT: C 982 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7107 (pp) REVERT: C 1009 MET cc_start: 0.8407 (mmm) cc_final: 0.7477 (mmm) REVERT: B 304 MET cc_start: 0.8330 (tpt) cc_final: 0.8016 (tpp) REVERT: B 353 LEU cc_start: 0.8494 (mt) cc_final: 0.8153 (tt) REVERT: D 145 TYR cc_start: 0.7066 (m-80) cc_final: 0.6363 (m-80) REVERT: D 303 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8579 (t80) outliers start: 87 outliers final: 62 residues processed: 418 average time/residue: 0.1358 time to fit residues: 96.2094 Evaluate side-chains 401 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 333 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1049 ILE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 891 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 268 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 159 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 316 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 771 HIS ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100923 restraints weight = 132904.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.101677 restraints weight = 58795.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103425 restraints weight = 42047.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103754 restraints weight = 33761.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104297 restraints weight = 30859.370| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27688 Z= 0.150 Angle : 0.619 14.185 37567 Z= 0.307 Chirality : 0.042 0.214 4302 Planarity : 0.004 0.054 4717 Dihedral : 4.425 52.481 3622 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.38 % Allowed : 33.21 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3351 helix: 0.24 (0.14), residues: 1494 sheet: -1.51 (0.30), residues: 351 loop : -1.44 (0.16), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 393 TYR 0.014 0.001 TYR C 401 PHE 0.029 0.001 PHE B 131 TRP 0.017 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00347 (27688) covalent geometry : angle 0.61881 (37567) hydrogen bonds : bond 0.03639 ( 1057) hydrogen bonds : angle 5.11797 ( 2956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 342 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: A 279 TYR cc_start: 0.8139 (m-80) cc_final: 0.7435 (m-80) REVERT: A 521 GLU cc_start: 0.8598 (mp0) cc_final: 0.8361 (pm20) REVERT: A 564 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (tt) REVERT: C 159 PHE cc_start: 0.8852 (t80) cc_final: 0.7938 (m-80) REVERT: C 303 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8422 (t80) REVERT: C 799 MET cc_start: 0.8263 (tpp) cc_final: 0.7848 (tpt) REVERT: C 982 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7209 (pp) REVERT: C 1009 MET cc_start: 0.8364 (mmm) cc_final: 0.7513 (mmm) REVERT: B 353 LEU cc_start: 0.8488 (mt) cc_final: 0.8134 (tt) REVERT: B 393 ARG cc_start: 0.8380 (ptp90) cc_final: 0.8124 (ptp-170) REVERT: D 145 TYR cc_start: 0.7097 (m-80) cc_final: 0.6415 (m-80) REVERT: D 303 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8523 (t80) outliers start: 100 outliers final: 78 residues processed: 417 average time/residue: 0.1276 time to fit residues: 90.7764 Evaluate side-chains 414 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 331 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 192 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 264 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.139911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100085 restraints weight = 151076.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.102392 restraints weight = 64959.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.103573 restraints weight = 44143.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104819 restraints weight = 34916.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105622 restraints weight = 30353.142| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27688 Z= 0.146 Angle : 0.630 15.340 37567 Z= 0.310 Chirality : 0.042 0.202 4302 Planarity : 0.004 0.054 4717 Dihedral : 4.442 53.379 3622 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.61 % Allowed : 33.14 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.15), residues: 3351 helix: 0.25 (0.14), residues: 1491 sheet: -1.51 (0.30), residues: 351 loop : -1.44 (0.16), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 393 TYR 0.015 0.001 TYR C 279 PHE 0.034 0.001 PHE B 131 TRP 0.017 0.001 TRP C 176 HIS 0.006 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00337 (27688) covalent geometry : angle 0.62982 (37567) hydrogen bonds : bond 0.03613 ( 1057) hydrogen bonds : angle 5.12159 ( 2956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 337 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: A 279 TYR cc_start: 0.8137 (m-80) cc_final: 0.7413 (m-80) REVERT: A 521 GLU cc_start: 0.8579 (mp0) cc_final: 0.8364 (pm20) REVERT: A 564 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 159 PHE cc_start: 0.8855 (t80) cc_final: 0.7943 (m-80) REVERT: C 303 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8419 (t80) REVERT: C 799 MET cc_start: 0.8189 (tpp) cc_final: 0.7758 (tpt) REVERT: C 982 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7202 (pp) REVERT: C 1009 MET cc_start: 0.8335 (mmm) cc_final: 0.7519 (mmm) REVERT: B 353 LEU cc_start: 0.8495 (mt) cc_final: 0.8139 (tt) REVERT: B 393 ARG cc_start: 0.8350 (ptp90) cc_final: 0.8082 (ptp-170) REVERT: D 145 TYR cc_start: 0.7200 (m-80) cc_final: 0.6515 (m-80) REVERT: D 303 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8516 (t80) outliers start: 107 outliers final: 88 residues processed: 415 average time/residue: 0.1402 time to fit residues: 99.1925 Evaluate side-chains 425 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 332 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 883 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 21 MET Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 388 GLU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 790 ARG Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 879 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1000 PHE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 876 ILE Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 266 optimal weight: 0.0770 chunk 181 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 226 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 320 optimal weight: 7.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 957 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.142445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102915 restraints weight = 127335.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105384 restraints weight = 54282.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106589 restraints weight = 36225.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107085 restraints weight = 30720.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107889 restraints weight = 26983.980| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27688 Z= 0.107 Angle : 0.619 16.789 37567 Z= 0.301 Chirality : 0.042 0.218 4302 Planarity : 0.004 0.054 4717 Dihedral : 4.304 56.634 3622 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.78 % Allowed : 33.88 % Favored : 63.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.15), residues: 3351 helix: 0.30 (0.14), residues: 1492 sheet: -1.36 (0.29), residues: 362 loop : -1.42 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 393 TYR 0.012 0.001 TYR C 279 PHE 0.035 0.001 PHE B 131 TRP 0.016 0.001 TRP C 176 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00238 (27688) covalent geometry : angle 0.61875 (37567) hydrogen bonds : bond 0.03293 ( 1057) hydrogen bonds : angle 4.97731 ( 2956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 352 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TRP cc_start: 0.6940 (m100) cc_final: 0.5441 (m100) REVERT: A 276 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: A 279 TYR cc_start: 0.8104 (m-80) cc_final: 0.7390 (m-80) REVERT: A 564 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8426 (tt) REVERT: C 159 PHE cc_start: 0.8903 (t80) cc_final: 0.8014 (m-80) REVERT: C 160 PHE cc_start: 0.8370 (m-80) cc_final: 0.8072 (m-80) REVERT: C 303 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8393 (t80) REVERT: C 423 LEU cc_start: 0.8999 (mp) cc_final: 0.8763 (mp) REVERT: C 799 MET cc_start: 0.8158 (tpp) cc_final: 0.7713 (tpt) REVERT: C 982 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7021 (pp) REVERT: C 1009 MET cc_start: 0.8303 (mmm) cc_final: 0.7942 (mmm) REVERT: B 219 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8262 (mp0) REVERT: B 353 LEU cc_start: 0.8481 (mt) cc_final: 0.8124 (tt) REVERT: B 558 PHE cc_start: 0.6929 (t80) cc_final: 0.6572 (t80) REVERT: B 1051 CYS cc_start: 0.7871 (m) cc_final: 0.7588 (m) REVERT: B 1053 MET cc_start: 0.7414 (mmm) cc_final: 0.6792 (mmm) REVERT: D 145 TYR cc_start: 0.7162 (m-80) cc_final: 0.6480 (m-80) REVERT: D 303 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8524 (t80) REVERT: D 1009 MET cc_start: 0.7942 (tpp) cc_final: 0.7497 (mmm) outliers start: 82 outliers final: 67 residues processed: 407 average time/residue: 0.1317 time to fit residues: 90.8762 Evaluate side-chains 413 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 341 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 380 ASN Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 9 optimal weight: 20.0000 chunk 336 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 184 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 320 optimal weight: 3.9990 chunk 250 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 771 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.101467 restraints weight = 115636.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104259 restraints weight = 51894.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105113 restraints weight = 34655.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.105520 restraints weight = 32342.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106379 restraints weight = 28262.016| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3429 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27688 Z= 0.113 Angle : 0.624 16.546 37567 Z= 0.303 Chirality : 0.042 0.224 4302 Planarity : 0.004 0.054 4717 Dihedral : 4.160 50.772 3620 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 2.54 % Allowed : 33.98 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.15), residues: 3351 helix: 0.33 (0.14), residues: 1492 sheet: -1.33 (0.29), residues: 352 loop : -1.40 (0.16), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.012 0.001 TYR C 279 PHE 0.035 0.001 PHE B 131 TRP 0.017 0.001 TRP C 176 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00255 (27688) covalent geometry : angle 0.62360 (37567) hydrogen bonds : bond 0.03274 ( 1057) hydrogen bonds : angle 4.95554 ( 2956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6702 Ramachandran restraints generated. 3351 Oldfield, 0 Emsley, 3351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TRP cc_start: 0.7214 (m100) cc_final: 0.5774 (m100) REVERT: A 276 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8233 (pm20) REVERT: A 279 TYR cc_start: 0.8092 (m-80) cc_final: 0.7369 (m-80) REVERT: A 520 GLU cc_start: 0.6526 (pm20) cc_final: 0.5333 (pm20) REVERT: A 521 GLU cc_start: 0.7951 (mp0) cc_final: 0.7676 (mp0) REVERT: A 564 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (tt) REVERT: C 154 MET cc_start: 0.2738 (mmt) cc_final: 0.2431 (mmp) REVERT: C 159 PHE cc_start: 0.8911 (t80) cc_final: 0.8053 (m-80) REVERT: C 160 PHE cc_start: 0.8320 (m-80) cc_final: 0.7871 (m-80) REVERT: C 303 PHE cc_start: 0.8928 (OUTLIER) cc_final: 0.8385 (t80) REVERT: C 423 LEU cc_start: 0.9025 (mp) cc_final: 0.8807 (mp) REVERT: C 799 MET cc_start: 0.8079 (tpp) cc_final: 0.7621 (tpt) REVERT: C 982 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6991 (pp) REVERT: C 1009 MET cc_start: 0.8278 (mmm) cc_final: 0.7952 (mmm) REVERT: B 210 ARG cc_start: 0.7534 (pmt-80) cc_final: 0.7139 (pmt-80) REVERT: B 219 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8263 (mp0) REVERT: B 353 LEU cc_start: 0.8477 (mt) cc_final: 0.8115 (tt) REVERT: B 1051 CYS cc_start: 0.7836 (m) cc_final: 0.7556 (m) REVERT: B 1053 MET cc_start: 0.7429 (mmm) cc_final: 0.6816 (mmm) REVERT: D 145 TYR cc_start: 0.7162 (m-80) cc_final: 0.6515 (m-80) REVERT: D 303 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8488 (t80) REVERT: D 1009 MET cc_start: 0.7994 (tpp) cc_final: 0.7534 (mmm) outliers start: 75 outliers final: 66 residues processed: 400 average time/residue: 0.1320 time to fit residues: 89.9745 Evaluate side-chains 415 residues out of total 2991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 344 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 198 TYR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 365 HIS Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 513 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 874 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 975 CYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain C residue 148 PHE Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 797 CYS Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 906 THR Chi-restraints excluded: chain C residue 924 MET Chi-restraints excluded: chain C residue 937 ILE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain B residue 120 PHE Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 727 VAL Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 891 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 229 THR Chi-restraints excluded: chain D residue 275 TRP Chi-restraints excluded: chain D residue 303 PHE Chi-restraints excluded: chain D residue 306 PHE Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 449 ASN Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain D residue 545 PHE Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 600 SER Chi-restraints excluded: chain D residue 891 LEU Chi-restraints excluded: chain D residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 270 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 221 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 279 optimal weight: 0.6980 chunk 64 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 771 HIS C 957 ASN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** 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 = 0.4000 r_free = 0.4000 target = 0.143620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105934 restraints weight = 133542.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106982 restraints weight = 57507.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108370 restraints weight = 42079.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109264 restraints weight = 32208.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110070 restraints weight = 28354.173| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27688 Z= 0.105 Angle : 0.615 16.418 37567 Z= 0.299 Chirality : 0.041 0.192 4302 Planarity : 0.004 0.054 4717 Dihedral : 4.081 51.621 3620 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.61 % Allowed : 33.88 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.15), residues: 3351 helix: 0.34 (0.14), residues: 1497 sheet: -1.22 (0.29), residues: 359 loop : -1.42 (0.16), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 742 TYR 0.011 0.001 TYR D1007 PHE 0.035 0.001 PHE B 131 TRP 0.017 0.001 TRP C 178 HIS 0.007 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00230 (27688) covalent geometry : angle 0.61501 (37567) hydrogen bonds : bond 0.03116 ( 1057) hydrogen bonds : angle 4.89985 ( 2956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.04 seconds wall clock time: 76 minutes 18.03 seconds (4578.03 seconds total)