Starting phenix.real_space_refine on Mon May 26 15:43:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.map" model { file = "/net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v3g_21036/05_2025/6v3g_21036.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.006 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 192 5.16 5 C 18456 2.51 5 N 4680 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28520 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 895, 7130 Classifications: {'peptide': 895} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 866} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: C, B, D Time building chain proxies: 17.55, per 1000 atoms: 0.62 Number of scatterers: 28520 At special positions: 0 Unit cell: (144.3, 144.3, 135.2, 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 192 16.00 O 5192 8.00 N 4680 7.00 C 18456 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: 5.99 Conformation dependent library (CDL) restraints added in 3.2 seconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6800 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 49.4% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU B 179 " --> pdb=" O TRP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 211 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 215 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 223 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU B 324 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE B 494 " --> pdb=" O LYS B 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL B 605 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 607 " --> pdb=" O LYS B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 610 No H-bonds generated for 'chain 'B' and resid 608 through 610' Processing helix chain 'B' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS B 626 " --> pdb=" O PRO B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 742 No H-bonds generated for 'chain 'B' and resid 740 through 742' Processing helix chain 'B' and resid 759 through 764 Processing helix chain 'B' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU B 789 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 816 Processing helix chain 'B' and resid 817 through 830 Processing helix chain 'B' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 888 " --> pdb=" O ASP B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 884 through 888' Processing helix chain 'B' and resid 906 through 912 Processing helix chain 'B' and resid 919 through 930 removed outlier: 3.751A pdb=" N LEU B 923 " --> pdb=" O VAL B 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 942 Processing helix chain 'B' and resid 946 through 954 Processing helix chain 'B' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR B1006 " --> pdb=" O LYS B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA B1020 " --> pdb=" O LEU B1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS B1021 " --> pdb=" O ARG B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1017 through 1021' Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.933A pdb=" N SER A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.822A pdb=" N ARG A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.528A pdb=" N LEU A 179 " --> pdb=" O TRP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 211 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 213 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 259 removed outlier: 3.529A pdb=" N SER A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 326 removed outlier: 3.796A pdb=" N GLU A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 3.708A pdb=" N ASN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 removed outlier: 3.580A pdb=" N HIS A 468 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 532 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.625A pdb=" N VAL A 605 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 607 " --> pdb=" O LYS A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 610 No H-bonds generated for 'chain 'A' and resid 608 through 610' Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS A 626 " --> pdb=" O PRO A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 742 No H-bonds generated for 'chain 'A' and resid 740 through 742' Processing helix chain 'A' and resid 759 through 764 Processing helix chain 'A' and resid 765 through 770 removed outlier: 5.433A pdb=" N GLU A 768 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'A' and resid 817 through 830 Processing helix chain 'A' and resid 872 through 876 removed outlier: 3.586A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 888 " --> pdb=" O ASP A 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 884 through 888' Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 942 Processing helix chain 'A' and resid 946 through 954 Processing helix chain 'A' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA A1020 " --> pdb=" O LEU A1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS A1021 " --> pdb=" O ARG A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1017 through 1021' Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 115 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL C 116 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.638A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.529A pdb=" N LEU C 179 " --> pdb=" O TRP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.632A pdb=" N TYR C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 removed outlier: 3.765A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 211 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 215 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.533A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE C 223 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.990A pdb=" N MET C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS C 468 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE C 494 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 530 " --> pdb=" O LYS C 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL C 532 " --> pdb=" O TYR C 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL C 605 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 610 No H-bonds generated for 'chain 'C' and resid 608 through 610' Processing helix chain 'C' and resid 621 through 626 removed outlier: 3.551A pdb=" N LYS C 626 " --> pdb=" O PRO C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 742 No H-bonds generated for 'chain 'C' and resid 740 through 742' Processing helix chain 'C' and resid 759 through 764 Processing helix chain 'C' and resid 765 through 770 removed outlier: 5.434A pdb=" N GLU C 768 " --> pdb=" O ARG C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 792 removed outlier: 3.781A pdb=" N LEU C 789 " --> pdb=" O SER C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 816 Processing helix chain 'C' and resid 817 through 830 Processing helix chain 'C' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.717A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 888 " --> pdb=" O ASP C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 884 through 888' Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU C 923 " --> pdb=" O VAL C 919 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.197A 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 954 Processing helix chain 'C' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1021 removed outlier: 3.672A pdb=" N ALA C1020 " --> pdb=" O LEU C1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS C1021 " --> pdb=" O ARG C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1017 through 1021' Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.934A pdb=" N SER D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.916A pdb=" N SER D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 removed outlier: 3.823A pdb=" N ARG D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL D 116 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.639A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.530A pdb=" N LEU D 179 " --> pdb=" O TRP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 188 removed outlier: 4.385A pdb=" N ASP D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 200 removed outlier: 4.631A pdb=" N TYR D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.766A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 211 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 215 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.532A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 224 " --> pdb=" O ILE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 259 removed outlier: 3.528A pdb=" N SER D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.989A pdb=" N MET D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 318 removed outlier: 3.565A pdb=" N LEU D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.797A pdb=" N GLU D 324 " --> pdb=" O PRO D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 364 removed outlier: 3.709A pdb=" N ASN D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.892A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 removed outlier: 3.581A pdb=" N HIS D 468 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.830A pdb=" N ILE D 494 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 510 removed outlier: 3.596A pdb=" N MET D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 removed outlier: 3.768A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 530 " --> pdb=" O LYS D 526 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 532 " --> pdb=" O TYR D 528 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 601 through 607 removed outlier: 3.626A pdb=" N VAL D 605 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 607 " --> pdb=" O LYS D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 610 No H-bonds generated for 'chain 'D' and resid 608 through 610' Processing helix chain 'D' and resid 621 through 626 removed outlier: 3.550A pdb=" N LYS D 626 " --> pdb=" O PRO D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 742 No H-bonds generated for 'chain 'D' and resid 740 through 742' Processing helix chain 'D' and resid 759 through 764 Processing helix chain 'D' and resid 765 through 770 removed outlier: 5.435A pdb=" N GLU D 768 " --> pdb=" O ARG D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 785 through 792 removed outlier: 3.780A pdb=" N LEU D 789 " --> pdb=" O SER D 785 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 816 Processing helix chain 'D' and resid 817 through 830 Processing helix chain 'D' and resid 872 through 876 removed outlier: 3.587A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.718A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 888 " --> pdb=" O ASP D 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 884 through 888' Processing helix chain 'D' and resid 906 through 912 Processing helix chain 'D' and resid 919 through 930 removed outlier: 3.752A pdb=" N LEU D 923 " --> pdb=" O VAL D 919 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.197A 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 954 Processing helix chain 'D' and resid 995 through 1008 removed outlier: 3.917A pdb=" N THR D1006 " --> pdb=" O LYS D1002 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1021 removed outlier: 3.671A pdb=" N ALA D1020 " --> pdb=" O LEU D1017 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N HIS D1021 " --> pdb=" O ARG D1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1017 through 1021' Processing sheet with id=AA1, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'B' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR B 570 " --> pdb=" O ARG B 578 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL B 719 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL B 757 " --> pdb=" O VAL B 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL B 721 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE B1050 " --> pdb=" O PHE B1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA7, first strand: chain 'A' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A 570 " --> pdb=" O ARG A 578 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL A 719 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL A 757 " --> pdb=" O VAL A 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL A 721 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 976 through 980 removed outlier: 6.498A pdb=" N PHE A1050 " --> pdb=" O PHE A1012 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB3, first strand: chain 'C' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR C 570 " --> pdb=" O ARG C 578 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL C 719 " --> pdb=" O VAL C 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 757 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 721 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE C1050 " --> pdb=" O PHE C1012 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AB8, first strand: chain 'D' and resid 398 through 401 removed outlier: 4.517A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 535 through 540 removed outlier: 4.338A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR D 570 " --> pdb=" O ARG D 578 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.494A pdb=" N VAL D 719 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL D 757 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 721 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 976 through 980 removed outlier: 6.497A pdb=" N PHE D1050 " --> pdb=" O PHE D1012 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 3012 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: 9.43 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6819 1.33 - 1.45: 6241 1.45 - 1.57: 15828 1.57 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 29172 Sorted by residual: bond pdb=" N ASN A 582 " pdb=" CA ASN A 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN B 582 " pdb=" CA ASN B 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN D 582 " pdb=" CA ASN D 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.03e+01 bond pdb=" N ASN C 582 " pdb=" CA ASN C 582 " ideal model delta sigma weight residual 1.457 1.486 -0.029 9.10e-03 1.21e+04 1.02e+01 bond pdb=" N ILE C 568 " pdb=" CA ILE C 568 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.11e-02 8.12e+03 9.99e+00 ... (remaining 29167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 35484 1.66 - 3.33: 3525 3.33 - 4.99: 458 4.99 - 6.66: 81 6.66 - 8.32: 32 Bond angle restraints: 39580 Sorted by residual: angle pdb=" N GLN D 807 " pdb=" CA GLN D 807 " pdb=" C GLN D 807 " ideal model delta sigma weight residual 112.89 106.80 6.09 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN A 807 " pdb=" CA GLN A 807 " pdb=" C GLN A 807 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.41e+01 angle pdb=" N GLN B 807 " pdb=" CA GLN B 807 " pdb=" C GLN B 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.40e+01 angle pdb=" N GLN C 807 " pdb=" CA GLN C 807 " pdb=" C GLN C 807 " ideal model delta sigma weight residual 112.89 106.82 6.07 1.24e+00 6.50e-01 2.39e+01 angle pdb=" O ILE C 625 " pdb=" C ILE C 625 " pdb=" N LYS C 626 " ideal model delta sigma weight residual 121.87 125.76 -3.89 9.70e-01 1.06e+00 1.61e+01 ... (remaining 39575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 16283 15.93 - 31.86: 757 31.86 - 47.79: 164 47.79 - 63.72: 32 63.72 - 79.65: 16 Dihedral angle restraints: 17252 sinusoidal: 6760 harmonic: 10492 Sorted by residual: dihedral pdb=" CA ARG C 742 " pdb=" C ARG C 742 " pdb=" N ALA C 743 " pdb=" CA ALA C 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 742 " pdb=" C ARG B 742 " pdb=" N ALA B 743 " pdb=" CA ALA B 743 " ideal model delta harmonic sigma weight residual 180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG A 742 " pdb=" C ARG A 742 " pdb=" N ALA A 743 " pdb=" CA ALA A 743 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 17249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2905 0.054 - 0.108: 1053 0.108 - 0.161: 354 0.161 - 0.215: 168 0.215 - 0.269: 44 Chirality restraints: 4524 Sorted by residual: chirality pdb=" CA ILE C 484 " pdb=" N ILE C 484 " pdb=" C ILE C 484 " pdb=" CB ILE C 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE A 484 " pdb=" N ILE A 484 " pdb=" C ILE A 484 " pdb=" CB ILE A 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ILE B 484 " pdb=" N ILE B 484 " pdb=" C ILE B 484 " pdb=" CB ILE B 484 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4521 not shown) Planarity restraints: 4984 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 246 " -0.020 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP A 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 246 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 246 " 0.020 2.00e-02 2.50e+03 1.64e-02 6.75e+00 pdb=" CG TRP C 246 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP C 246 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 246 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 246 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 246 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 246 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 246 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 246 " -0.020 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP D 246 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP D 246 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 246 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 246 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 246 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 246 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 246 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 246 " -0.002 2.00e-02 2.50e+03 ... (remaining 4981 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3354 2.75 - 3.29: 28552 3.29 - 3.82: 46798 3.82 - 4.36: 56132 4.36 - 4.90: 92504 Nonbonded interactions: 227340 Sorted by model distance: nonbonded pdb=" N GLU C 819 " pdb=" OE1 GLU C 819 " model vdw 2.211 3.120 nonbonded pdb=" N GLU B 819 " pdb=" OE1 GLU B 819 " model vdw 2.212 3.120 nonbonded pdb=" N GLU D 819 " pdb=" OE1 GLU D 819 " model vdw 2.212 3.120 nonbonded pdb=" N GLU A 819 " pdb=" OE1 GLU A 819 " model vdw 2.212 3.120 nonbonded pdb=" N ASP B 621 " pdb=" OD1 ASP B 621 " model vdw 2.217 3.120 ... (remaining 227335 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.040 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 58.350 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 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 : 0.008 0.080 29172 Z= 0.480 Angle : 1.052 8.322 39580 Z= 0.694 Chirality : 0.071 0.269 4524 Planarity : 0.006 0.052 4984 Dihedral : 10.567 79.651 10452 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.66 % Allowed : 4.95 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.13), residues: 3548 helix: -2.14 (0.11), residues: 1456 sheet: -2.15 (0.22), residues: 416 loop : -1.28 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 246 HIS 0.013 0.002 HIS A 379 PHE 0.030 0.003 PHE A1012 TYR 0.025 0.002 TYR D1015 ARG 0.009 0.001 ARG C1031 Details of bonding type rmsd hydrogen bonds : bond 0.20127 ( 1072) hydrogen bonds : angle 8.08360 ( 3012) covalent geometry : bond 0.00797 (29172) covalent geometry : angle 1.05218 (39580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 533 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.6227 (mpp) cc_final: 0.5948 (mpp) REVERT: B 491 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8624 (tp) REVERT: B 506 MET cc_start: 0.6557 (ttm) cc_final: 0.6079 (ttp) REVERT: B 627 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7881 (mtmm) REVERT: B 715 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8009 (pp) REVERT: B 795 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 998 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.7988 (p0) REVERT: A 21 MET cc_start: 0.6220 (mpp) cc_final: 0.5950 (mpp) REVERT: A 491 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 506 MET cc_start: 0.6560 (ttm) cc_final: 0.6088 (ttp) REVERT: A 627 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: A 715 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8013 (pp) REVERT: A 795 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8885 (p0) REVERT: A 998 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7981 (p0) REVERT: C 21 MET cc_start: 0.6224 (mpp) cc_final: 0.5951 (mpp) REVERT: C 491 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 506 MET cc_start: 0.6554 (ttm) cc_final: 0.6066 (ttp) REVERT: C 627 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7787 (mtmm) REVERT: C 715 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8004 (pp) REVERT: C 795 ASN cc_start: 0.9129 (OUTLIER) cc_final: 0.8875 (p0) REVERT: C 998 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8135 (p0) REVERT: D 21 MET cc_start: 0.6227 (mpp) cc_final: 0.5955 (mpp) REVERT: D 491 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 506 MET cc_start: 0.6548 (ttm) cc_final: 0.6069 (ttp) REVERT: D 627 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7804 (mtmm) REVERT: D 715 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8056 (pp) REVERT: D 795 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8899 (p0) REVERT: D 998 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7950 (p0) outliers start: 84 outliers final: 14 residues processed: 613 average time/residue: 0.3982 time to fit residues: 389.2261 Evaluate side-chains 292 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 HIS Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 627 LYS Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 795 ASN Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 627 LYS Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 795 ASN Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 627 LYS Chi-restraints excluded: chain C residue 632 ARG Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 795 ASN Chi-restraints excluded: chain C residue 800 CYS Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 350 HIS Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 627 LYS Chi-restraints excluded: chain D residue 632 ARG Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 795 ASN Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 1.9990 chunk 269 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 169 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN B 379 HIS B 394 HIS B 501 GLN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN A 379 HIS A 394 HIS A 501 GLN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN C 222 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN C 379 HIS C 394 HIS C 501 GLN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 GLN D 379 HIS D 394 HIS D 501 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.058315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.044124 restraints weight = 142239.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.045531 restraints weight = 81130.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.046429 restraints weight = 54629.102| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 29172 Z= 0.316 Angle : 0.788 10.189 39580 Z= 0.403 Chirality : 0.045 0.143 4524 Planarity : 0.006 0.053 4984 Dihedral : 6.662 55.802 3908 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.54 % Allowed : 11.87 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3548 helix: -0.89 (0.12), residues: 1496 sheet: -1.58 (0.24), residues: 456 loop : -0.70 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 246 HIS 0.006 0.002 HIS D 451 PHE 0.029 0.002 PHE D 303 TYR 0.016 0.002 TYR B 928 ARG 0.007 0.001 ARG D 632 Details of bonding type rmsd hydrogen bonds : bond 0.04575 ( 1072) hydrogen bonds : angle 5.95197 ( 3012) covalent geometry : bond 0.00660 (29172) covalent geometry : angle 0.78848 (39580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 290 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7433 (mpp) cc_final: 0.6892 (mpp) REVERT: B 213 ARG cc_start: 0.8987 (mtt180) cc_final: 0.8084 (mmt-90) REVERT: B 318 TYR cc_start: 0.8162 (t80) cc_final: 0.7708 (t80) REVERT: B 460 MET cc_start: 0.8368 (mmm) cc_final: 0.7575 (mmm) REVERT: B 513 MET cc_start: 0.9046 (mmm) cc_final: 0.8538 (mmt) REVERT: B 565 MET cc_start: 0.8732 (ttp) cc_final: 0.8488 (ptt) REVERT: B 580 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9417 (tt) REVERT: B 715 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8726 (pp) REVERT: B 726 ASP cc_start: 0.9141 (t70) cc_final: 0.8865 (p0) REVERT: B 998 ASP cc_start: 0.9219 (OUTLIER) cc_final: 0.8910 (p0) REVERT: A 21 MET cc_start: 0.7429 (mpp) cc_final: 0.6886 (mpp) REVERT: A 213 ARG cc_start: 0.8972 (mtt180) cc_final: 0.8085 (mmt-90) REVERT: A 318 TYR cc_start: 0.8156 (t80) cc_final: 0.7699 (t80) REVERT: A 460 MET cc_start: 0.8412 (mmm) cc_final: 0.7621 (mmm) REVERT: A 513 MET cc_start: 0.9032 (mmm) cc_final: 0.8535 (mmt) REVERT: A 565 MET cc_start: 0.8744 (ttp) cc_final: 0.8509 (ptt) REVERT: A 580 LEU cc_start: 0.9683 (OUTLIER) cc_final: 0.9423 (tt) REVERT: A 715 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 726 ASP cc_start: 0.9148 (t70) cc_final: 0.8873 (p0) REVERT: A 998 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8925 (p0) REVERT: C 21 MET cc_start: 0.7453 (mpp) cc_final: 0.6911 (mpp) REVERT: C 213 ARG cc_start: 0.8978 (mtt180) cc_final: 0.8071 (mmt-90) REVERT: C 252 PHE cc_start: 0.9628 (t80) cc_final: 0.9062 (t80) REVERT: C 303 PHE cc_start: 0.9419 (t80) cc_final: 0.8750 (t80) REVERT: C 318 TYR cc_start: 0.8152 (t80) cc_final: 0.7833 (t80) REVERT: C 460 MET cc_start: 0.8390 (mmm) cc_final: 0.7618 (mmm) REVERT: C 513 MET cc_start: 0.9057 (mmm) cc_final: 0.8660 (mmt) REVERT: C 565 MET cc_start: 0.8763 (ttp) cc_final: 0.8555 (ptt) REVERT: C 580 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9411 (tt) REVERT: C 715 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 726 ASP cc_start: 0.9140 (t70) cc_final: 0.8875 (p0) REVERT: C 879 ILE cc_start: 0.9584 (mt) cc_final: 0.9360 (tp) REVERT: C 998 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8877 (p0) REVERT: D 21 MET cc_start: 0.7453 (mpp) cc_final: 0.6904 (mpp) REVERT: D 213 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8073 (mmt-90) REVERT: D 252 PHE cc_start: 0.9626 (t80) cc_final: 0.9063 (t80) REVERT: D 303 PHE cc_start: 0.9434 (t80) cc_final: 0.8772 (t80) REVERT: D 318 TYR cc_start: 0.8174 (t80) cc_final: 0.7857 (t80) REVERT: D 442 MET cc_start: 0.9804 (mmm) cc_final: 0.9575 (tpp) REVERT: D 460 MET cc_start: 0.8339 (mmm) cc_final: 0.7557 (mmm) REVERT: D 513 MET cc_start: 0.9053 (mmm) cc_final: 0.8656 (mmt) REVERT: D 565 MET cc_start: 0.8757 (ttp) cc_final: 0.8542 (ptt) REVERT: D 580 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9414 (tt) REVERT: D 715 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8723 (pp) REVERT: D 726 ASP cc_start: 0.9141 (t70) cc_final: 0.8868 (p0) REVERT: D 998 ASP cc_start: 0.9183 (OUTLIER) cc_final: 0.8884 (p0) outliers start: 80 outliers final: 30 residues processed: 350 average time/residue: 0.3541 time to fit residues: 208.9742 Evaluate side-chains 299 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 257 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 807 GLN Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 574 ASN Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 807 GLN Chi-restraints excluded: chain D residue 998 ASP Chi-restraints excluded: chain D residue 1011 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 265 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 331 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 258 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.060082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.045953 restraints weight = 137437.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.047239 restraints weight = 77871.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.048338 restraints weight = 51538.355| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29172 Z= 0.124 Angle : 0.617 7.798 39580 Z= 0.313 Chirality : 0.043 0.182 4524 Planarity : 0.004 0.048 4984 Dihedral : 5.614 48.031 3856 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 11.07 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3548 helix: -0.51 (0.13), residues: 1488 sheet: -1.92 (0.24), residues: 420 loop : -0.42 (0.17), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 246 HIS 0.004 0.001 HIS C 350 PHE 0.027 0.002 PHE D 832 TYR 0.013 0.001 TYR C 279 ARG 0.006 0.000 ARG C 786 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 1072) hydrogen bonds : angle 5.47477 ( 3012) covalent geometry : bond 0.00279 (29172) covalent geometry : angle 0.61723 (39580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 317 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7234 (mpp) cc_final: 0.6583 (mpp) REVERT: B 154 MET cc_start: 0.7895 (mpp) cc_final: 0.7418 (mpp) REVERT: B 164 PHE cc_start: 0.7494 (p90) cc_final: 0.7006 (p90) REVERT: B 213 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8132 (mmt-90) REVERT: B 252 PHE cc_start: 0.9497 (t80) cc_final: 0.9137 (t80) REVERT: B 482 ASP cc_start: 0.8821 (m-30) cc_final: 0.8621 (m-30) REVERT: B 513 MET cc_start: 0.8823 (mmm) cc_final: 0.8614 (mmm) REVERT: B 565 MET cc_start: 0.8912 (ttp) cc_final: 0.8406 (ptt) REVERT: B 580 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9404 (tt) REVERT: B 691 MET cc_start: 0.9236 (mmm) cc_final: 0.9020 (mmm) REVERT: B 715 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8670 (pp) REVERT: B 726 ASP cc_start: 0.9153 (t70) cc_final: 0.8856 (p0) REVERT: B 913 THR cc_start: 0.9686 (p) cc_final: 0.9403 (t) REVERT: B 950 GLU cc_start: 0.9211 (tt0) cc_final: 0.8946 (mt-10) REVERT: B 998 ASP cc_start: 0.9257 (OUTLIER) cc_final: 0.8921 (p0) REVERT: A 21 MET cc_start: 0.7221 (mpp) cc_final: 0.6563 (mpp) REVERT: A 154 MET cc_start: 0.7907 (mpp) cc_final: 0.7425 (mpp) REVERT: A 164 PHE cc_start: 0.7505 (p90) cc_final: 0.7014 (p90) REVERT: A 213 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8137 (mmt-90) REVERT: A 252 PHE cc_start: 0.9500 (t80) cc_final: 0.9134 (t80) REVERT: A 460 MET cc_start: 0.8629 (mmm) cc_final: 0.7635 (mmm) REVERT: A 513 MET cc_start: 0.8852 (mmm) cc_final: 0.8612 (mmm) REVERT: A 565 MET cc_start: 0.8903 (ttp) cc_final: 0.8396 (ptt) REVERT: A 580 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9404 (tt) REVERT: A 691 MET cc_start: 0.9243 (mmm) cc_final: 0.9031 (mmm) REVERT: A 715 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8702 (pp) REVERT: A 726 ASP cc_start: 0.9128 (t70) cc_final: 0.8806 (p0) REVERT: A 913 THR cc_start: 0.9681 (p) cc_final: 0.9404 (t) REVERT: A 950 GLU cc_start: 0.9217 (tt0) cc_final: 0.8944 (mt-10) REVERT: A 998 ASP cc_start: 0.9244 (OUTLIER) cc_final: 0.8912 (p0) REVERT: C 21 MET cc_start: 0.7285 (mpp) cc_final: 0.6639 (mpp) REVERT: C 154 MET cc_start: 0.7888 (mpp) cc_final: 0.7416 (mpp) REVERT: C 164 PHE cc_start: 0.7489 (p90) cc_final: 0.7001 (p90) REVERT: C 213 ARG cc_start: 0.8960 (mtt180) cc_final: 0.8253 (mmt-90) REVERT: C 252 PHE cc_start: 0.9580 (t80) cc_final: 0.9064 (t80) REVERT: C 281 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9320 (mm) REVERT: C 282 MET cc_start: 0.9615 (tpp) cc_final: 0.9103 (tpp) REVERT: C 460 MET cc_start: 0.8554 (mmm) cc_final: 0.7136 (tmm) REVERT: C 482 ASP cc_start: 0.8815 (m-30) cc_final: 0.8613 (m-30) REVERT: C 513 MET cc_start: 0.8829 (mmm) cc_final: 0.8602 (mmm) REVERT: C 565 MET cc_start: 0.8916 (ttp) cc_final: 0.8473 (ptt) REVERT: C 580 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9378 (tt) REVERT: C 691 MET cc_start: 0.9245 (mmm) cc_final: 0.9026 (mmm) REVERT: C 715 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 726 ASP cc_start: 0.9169 (t70) cc_final: 0.8885 (p0) REVERT: C 950 GLU cc_start: 0.9214 (tt0) cc_final: 0.8942 (mt-10) REVERT: C 998 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8909 (p0) REVERT: D 21 MET cc_start: 0.7256 (mpp) cc_final: 0.6606 (mpp) REVERT: D 154 MET cc_start: 0.7890 (mpp) cc_final: 0.7415 (mpp) REVERT: D 164 PHE cc_start: 0.7487 (p90) cc_final: 0.7036 (p90) REVERT: D 213 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8167 (tpp-160) REVERT: D 252 PHE cc_start: 0.9579 (t80) cc_final: 0.8963 (t80) REVERT: D 281 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9323 (mm) REVERT: D 303 PHE cc_start: 0.9385 (t80) cc_final: 0.8570 (t80) REVERT: D 442 MET cc_start: 0.9683 (mmm) cc_final: 0.9447 (tpp) REVERT: D 460 MET cc_start: 0.8571 (mmm) cc_final: 0.7573 (mmm) REVERT: D 482 ASP cc_start: 0.8833 (m-30) cc_final: 0.8624 (m-30) REVERT: D 513 MET cc_start: 0.8819 (mmm) cc_final: 0.8596 (mmm) REVERT: D 565 MET cc_start: 0.8919 (ttp) cc_final: 0.8481 (ptt) REVERT: D 580 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9379 (tt) REVERT: D 691 MET cc_start: 0.9249 (mmm) cc_final: 0.9029 (mmm) REVERT: D 715 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8675 (pp) REVERT: D 726 ASP cc_start: 0.9167 (t70) cc_final: 0.8885 (p0) REVERT: D 913 THR cc_start: 0.9710 (p) cc_final: 0.9427 (t) REVERT: D 950 GLU cc_start: 0.9232 (tt0) cc_final: 0.8952 (mt-10) REVERT: D 998 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8921 (p0) outliers start: 75 outliers final: 22 residues processed: 372 average time/residue: 0.3275 time to fit residues: 207.4468 Evaluate side-chains 309 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 3.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 294 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 271 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 40.0000 chunk 328 optimal weight: 3.9990 chunk 291 optimal weight: 0.0570 chunk 5 optimal weight: 3.9990 chunk 148 optimal weight: 0.0770 chunk 332 optimal weight: 8.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.059687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.045530 restraints weight = 139192.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.046930 restraints weight = 79956.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.048024 restraints weight = 52993.508| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29172 Z= 0.135 Angle : 0.595 10.691 39580 Z= 0.301 Chirality : 0.042 0.232 4524 Planarity : 0.004 0.048 4984 Dihedral : 5.367 48.632 3856 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.70 % Allowed : 11.55 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3548 helix: -0.14 (0.13), residues: 1480 sheet: -1.80 (0.25), residues: 420 loop : -0.33 (0.17), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 246 HIS 0.004 0.001 HIS D 350 PHE 0.018 0.001 PHE D 164 TYR 0.011 0.001 TYR D 279 ARG 0.006 0.001 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1072) hydrogen bonds : angle 5.31120 ( 3012) covalent geometry : bond 0.00309 (29172) covalent geometry : angle 0.59517 (39580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 276 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7402 (mpp) cc_final: 0.6760 (mpp) REVERT: B 104 MET cc_start: 0.5671 (mmm) cc_final: 0.5206 (mmm) REVERT: B 154 MET cc_start: 0.7958 (mpp) cc_final: 0.7575 (mpp) REVERT: B 209 LEU cc_start: 0.9518 (mt) cc_final: 0.9261 (mt) REVERT: B 213 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8016 (mmt-90) REVERT: B 252 PHE cc_start: 0.9518 (t80) cc_final: 0.9091 (t80) REVERT: B 482 ASP cc_start: 0.8821 (m-30) cc_final: 0.8567 (m-30) REVERT: B 691 MET cc_start: 0.9239 (mmm) cc_final: 0.8600 (tpp) REVERT: B 715 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8735 (pp) REVERT: B 726 ASP cc_start: 0.9104 (t70) cc_final: 0.8780 (p0) REVERT: B 913 THR cc_start: 0.9657 (p) cc_final: 0.9429 (t) REVERT: B 950 GLU cc_start: 0.9221 (tt0) cc_final: 0.8896 (mt-10) REVERT: B 972 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8491 (ppp80) REVERT: B 998 ASP cc_start: 0.9281 (OUTLIER) cc_final: 0.8948 (p0) REVERT: B 1012 PHE cc_start: 0.8059 (t80) cc_final: 0.7794 (t80) REVERT: A 21 MET cc_start: 0.7380 (mpp) cc_final: 0.6736 (mpp) REVERT: A 104 MET cc_start: 0.5673 (mmm) cc_final: 0.5204 (mmm) REVERT: A 154 MET cc_start: 0.7977 (mpp) cc_final: 0.7585 (mpp) REVERT: A 209 LEU cc_start: 0.9529 (mt) cc_final: 0.9264 (mt) REVERT: A 213 ARG cc_start: 0.8957 (mtt180) cc_final: 0.8025 (mmt-90) REVERT: A 252 PHE cc_start: 0.9522 (t80) cc_final: 0.9098 (t80) REVERT: A 282 MET cc_start: 0.9600 (tpp) cc_final: 0.9088 (tpp) REVERT: A 460 MET cc_start: 0.8806 (mmm) cc_final: 0.7924 (mmm) REVERT: A 691 MET cc_start: 0.9249 (mmm) cc_final: 0.8612 (tpp) REVERT: A 715 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 726 ASP cc_start: 0.9117 (t70) cc_final: 0.8807 (p0) REVERT: A 913 THR cc_start: 0.9650 (p) cc_final: 0.9426 (t) REVERT: A 950 GLU cc_start: 0.9227 (tt0) cc_final: 0.8940 (mt-10) REVERT: A 972 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8496 (ppp80) REVERT: A 998 ASP cc_start: 0.9300 (OUTLIER) cc_final: 0.8960 (p0) REVERT: A 1012 PHE cc_start: 0.8067 (t80) cc_final: 0.7807 (t80) REVERT: C 21 MET cc_start: 0.7405 (mpp) cc_final: 0.6759 (mpp) REVERT: C 154 MET cc_start: 0.7956 (mpp) cc_final: 0.7577 (mpp) REVERT: C 252 PHE cc_start: 0.9583 (t80) cc_final: 0.9018 (t80) REVERT: C 281 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9321 (mm) REVERT: C 282 MET cc_start: 0.9605 (tpp) cc_final: 0.9045 (tpp) REVERT: C 303 PHE cc_start: 0.9347 (t80) cc_final: 0.8720 (t80) REVERT: C 482 ASP cc_start: 0.8838 (m-30) cc_final: 0.8571 (m-30) REVERT: C 691 MET cc_start: 0.9246 (mmm) cc_final: 0.8977 (mmm) REVERT: C 715 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8774 (pp) REVERT: C 726 ASP cc_start: 0.9100 (t70) cc_final: 0.8788 (p0) REVERT: C 799 MET cc_start: 0.8066 (tpp) cc_final: 0.7731 (tpp) REVERT: C 830 MET cc_start: 0.7902 (tpp) cc_final: 0.7668 (tpp) REVERT: C 950 GLU cc_start: 0.9214 (tt0) cc_final: 0.8894 (mt-10) REVERT: C 972 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.8474 (ppp80) REVERT: C 998 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8890 (p0) REVERT: C 1012 PHE cc_start: 0.8043 (t80) cc_final: 0.7801 (t80) REVERT: D 21 MET cc_start: 0.7403 (mpp) cc_final: 0.6751 (mpp) REVERT: D 154 MET cc_start: 0.7953 (mpp) cc_final: 0.7571 (mpp) REVERT: D 252 PHE cc_start: 0.9580 (t80) cc_final: 0.9030 (t80) REVERT: D 281 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9342 (mm) REVERT: D 282 MET cc_start: 0.9640 (tpp) cc_final: 0.9136 (tpp) REVERT: D 303 PHE cc_start: 0.9356 (t80) cc_final: 0.8740 (t80) REVERT: D 460 MET cc_start: 0.8742 (mmm) cc_final: 0.7743 (mmm) REVERT: D 482 ASP cc_start: 0.8855 (m-30) cc_final: 0.8589 (m-30) REVERT: D 691 MET cc_start: 0.9246 (mmm) cc_final: 0.8975 (mmm) REVERT: D 715 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8748 (pp) REVERT: D 726 ASP cc_start: 0.9109 (t70) cc_final: 0.8793 (p0) REVERT: D 913 THR cc_start: 0.9693 (p) cc_final: 0.9467 (t) REVERT: D 950 GLU cc_start: 0.9235 (tt0) cc_final: 0.8931 (mt-10) REVERT: D 972 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8476 (ppp80) REVERT: D 998 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8896 (p0) REVERT: D 1012 PHE cc_start: 0.8058 (t80) cc_final: 0.7833 (t80) outliers start: 85 outliers final: 29 residues processed: 340 average time/residue: 0.3311 time to fit residues: 190.9749 Evaluate side-chains 311 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 739 MET Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 739 MET Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 739 MET Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 173 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 350 optimal weight: 10.0000 chunk 329 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 273 optimal weight: 20.0000 chunk 230 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.059251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.045141 restraints weight = 139364.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.046496 restraints weight = 80151.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.047207 restraints weight = 54487.584| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29172 Z= 0.148 Angle : 0.593 8.861 39580 Z= 0.300 Chirality : 0.042 0.252 4524 Planarity : 0.004 0.047 4984 Dihedral : 5.251 50.066 3856 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.22 % Allowed : 12.28 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 3548 helix: -0.04 (0.13), residues: 1512 sheet: -1.70 (0.25), residues: 416 loop : -0.41 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 246 HIS 0.003 0.001 HIS D 254 PHE 0.016 0.001 PHE D 164 TYR 0.010 0.001 TYR D 279 ARG 0.005 0.000 ARG D 443 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 1072) hydrogen bonds : angle 5.25140 ( 3012) covalent geometry : bond 0.00333 (29172) covalent geometry : angle 0.59269 (39580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7336 (mpp) cc_final: 0.6642 (mpp) REVERT: B 104 MET cc_start: 0.5745 (mmm) cc_final: 0.5451 (mmm) REVERT: B 154 MET cc_start: 0.8029 (mpp) cc_final: 0.7617 (mpp) REVERT: B 209 LEU cc_start: 0.9505 (mt) cc_final: 0.9254 (mt) REVERT: B 213 ARG cc_start: 0.9008 (mtt180) cc_final: 0.8136 (mmt-90) REVERT: B 252 PHE cc_start: 0.9556 (t80) cc_final: 0.9083 (t80) REVERT: B 281 LEU cc_start: 0.9615 (mm) cc_final: 0.9340 (mm) REVERT: B 282 MET cc_start: 0.9500 (tpp) cc_final: 0.8964 (tpp) REVERT: B 460 MET cc_start: 0.8625 (mmm) cc_final: 0.8235 (mmm) REVERT: B 482 ASP cc_start: 0.8764 (m-30) cc_final: 0.8561 (m-30) REVERT: B 580 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9356 (tt) REVERT: B 691 MET cc_start: 0.9241 (mmm) cc_final: 0.8983 (mmm) REVERT: B 715 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 830 MET cc_start: 0.8854 (tpp) cc_final: 0.8334 (mmm) REVERT: B 913 THR cc_start: 0.9695 (p) cc_final: 0.9467 (t) REVERT: B 950 GLU cc_start: 0.9268 (tt0) cc_final: 0.8914 (mt-10) REVERT: B 972 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.8585 (ppp80) REVERT: B 998 ASP cc_start: 0.9272 (OUTLIER) cc_final: 0.8976 (p0) REVERT: B 1012 PHE cc_start: 0.8055 (t80) cc_final: 0.7823 (t80) REVERT: A 21 MET cc_start: 0.7316 (mpp) cc_final: 0.6620 (mpp) REVERT: A 154 MET cc_start: 0.8044 (mpp) cc_final: 0.7626 (mpp) REVERT: A 209 LEU cc_start: 0.9515 (mt) cc_final: 0.9258 (mt) REVERT: A 213 ARG cc_start: 0.8998 (mtt180) cc_final: 0.8073 (mmt-90) REVERT: A 252 PHE cc_start: 0.9558 (t80) cc_final: 0.9078 (t80) REVERT: A 281 LEU cc_start: 0.9622 (mm) cc_final: 0.9330 (mm) REVERT: A 282 MET cc_start: 0.9580 (tpp) cc_final: 0.9084 (tpp) REVERT: A 580 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9356 (tt) REVERT: A 691 MET cc_start: 0.9255 (mmm) cc_final: 0.8993 (mmm) REVERT: A 715 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8759 (pp) REVERT: A 830 MET cc_start: 0.8865 (tpp) cc_final: 0.8277 (mmm) REVERT: A 913 THR cc_start: 0.9690 (p) cc_final: 0.9460 (t) REVERT: A 950 GLU cc_start: 0.9236 (tt0) cc_final: 0.8892 (mt-10) REVERT: A 972 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8585 (ppp80) REVERT: A 998 ASP cc_start: 0.9302 (OUTLIER) cc_final: 0.9005 (p0) REVERT: A 1012 PHE cc_start: 0.8133 (t80) cc_final: 0.7917 (t80) REVERT: C 21 MET cc_start: 0.7361 (mpp) cc_final: 0.6667 (mpp) REVERT: C 104 MET cc_start: 0.5376 (mmm) cc_final: 0.5150 (mmm) REVERT: C 154 MET cc_start: 0.8021 (mpp) cc_final: 0.7616 (mpp) REVERT: C 213 ARG cc_start: 0.9060 (mtt180) cc_final: 0.8105 (mmt-90) REVERT: C 252 PHE cc_start: 0.9588 (t80) cc_final: 0.8834 (t80) REVERT: C 281 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.9346 (mm) REVERT: C 282 MET cc_start: 0.9585 (tpp) cc_final: 0.9029 (tpp) REVERT: C 303 PHE cc_start: 0.9362 (t80) cc_final: 0.8459 (t80) REVERT: C 482 ASP cc_start: 0.8802 (m-30) cc_final: 0.8534 (m-30) REVERT: C 691 MET cc_start: 0.9248 (mmm) cc_final: 0.8984 (mmm) REVERT: C 715 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8806 (pp) REVERT: C 799 MET cc_start: 0.8064 (tpp) cc_final: 0.7780 (tpp) REVERT: C 830 MET cc_start: 0.8138 (tpp) cc_final: 0.7791 (tpp) REVERT: C 950 GLU cc_start: 0.9270 (tt0) cc_final: 0.8878 (mt-10) REVERT: C 972 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8532 (ppp80) REVERT: C 998 ASP cc_start: 0.9259 (OUTLIER) cc_final: 0.8924 (p0) REVERT: D 21 MET cc_start: 0.7350 (mpp) cc_final: 0.6655 (mpp) REVERT: D 104 MET cc_start: 0.5411 (mmm) cc_final: 0.5183 (mmm) REVERT: D 154 MET cc_start: 0.8023 (mpp) cc_final: 0.7622 (mpp) REVERT: D 213 ARG cc_start: 0.9059 (mtt180) cc_final: 0.8085 (mmt-90) REVERT: D 252 PHE cc_start: 0.9587 (t80) cc_final: 0.8842 (t80) REVERT: D 281 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9353 (mm) REVERT: D 282 MET cc_start: 0.9629 (tpp) cc_final: 0.9110 (tpp) REVERT: D 303 PHE cc_start: 0.9367 (t80) cc_final: 0.8476 (t80) REVERT: D 482 ASP cc_start: 0.8786 (m-30) cc_final: 0.8472 (m-30) REVERT: D 580 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9355 (tt) REVERT: D 691 MET cc_start: 0.9253 (mmm) cc_final: 0.8984 (mmm) REVERT: D 715 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8756 (pp) REVERT: D 830 MET cc_start: 0.9109 (tpp) cc_final: 0.8613 (tpp) REVERT: D 913 THR cc_start: 0.9694 (p) cc_final: 0.9466 (t) REVERT: D 950 GLU cc_start: 0.9256 (tt0) cc_final: 0.8899 (mt-10) REVERT: D 972 ARG cc_start: 0.9310 (OUTLIER) cc_final: 0.8538 (ppp80) REVERT: D 998 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8927 (p0) REVERT: D 1012 PHE cc_start: 0.8127 (t80) cc_final: 0.7845 (t80) outliers start: 70 outliers final: 39 residues processed: 331 average time/residue: 0.3516 time to fit residues: 195.2394 Evaluate side-chains 314 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 741 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 79 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 345 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 chunk 267 optimal weight: 30.0000 chunk 277 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.058768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.044503 restraints weight = 140113.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045876 restraints weight = 81795.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046669 restraints weight = 55949.476| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29172 Z= 0.164 Angle : 0.597 8.932 39580 Z= 0.301 Chirality : 0.042 0.188 4524 Planarity : 0.004 0.047 4984 Dihedral : 5.163 51.044 3856 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.57 % Allowed : 12.47 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3548 helix: 0.16 (0.13), residues: 1512 sheet: -1.68 (0.25), residues: 416 loop : -0.38 (0.17), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 246 HIS 0.003 0.001 HIS D 451 PHE 0.024 0.001 PHE C1012 TYR 0.010 0.001 TYR A 279 ARG 0.004 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 1072) hydrogen bonds : angle 5.17451 ( 3012) covalent geometry : bond 0.00368 (29172) covalent geometry : angle 0.59706 (39580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 267 time to evaluate : 3.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 MET cc_start: 0.7382 (mpp) cc_final: 0.6665 (mpp) REVERT: B 104 MET cc_start: 0.5782 (mmm) cc_final: 0.5507 (mmm) REVERT: B 154 MET cc_start: 0.8062 (mpp) cc_final: 0.7641 (mpp) REVERT: B 209 LEU cc_start: 0.9502 (mt) cc_final: 0.9226 (mt) REVERT: B 213 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8064 (mmt-90) REVERT: B 252 PHE cc_start: 0.9627 (t80) cc_final: 0.9111 (t80) REVERT: B 281 LEU cc_start: 0.9620 (mm) cc_final: 0.9335 (mm) REVERT: B 282 MET cc_start: 0.9553 (tpp) cc_final: 0.9021 (tpp) REVERT: B 460 MET cc_start: 0.8549 (mmm) cc_final: 0.8284 (mmm) REVERT: B 482 ASP cc_start: 0.8764 (m-30) cc_final: 0.8550 (m-30) REVERT: B 580 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9378 (tt) REVERT: B 691 MET cc_start: 0.9246 (mmm) cc_final: 0.8996 (mmm) REVERT: B 726 ASP cc_start: 0.9147 (t70) cc_final: 0.8785 (p0) REVERT: B 830 MET cc_start: 0.8862 (tpp) cc_final: 0.8293 (mmm) REVERT: B 913 THR cc_start: 0.9700 (p) cc_final: 0.9475 (t) REVERT: B 950 GLU cc_start: 0.9291 (tt0) cc_final: 0.8885 (mt-10) REVERT: B 972 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.8615 (ppp80) REVERT: B 998 ASP cc_start: 0.9273 (OUTLIER) cc_final: 0.8968 (p0) REVERT: B 1012 PHE cc_start: 0.8100 (t80) cc_final: 0.7894 (t80) REVERT: A 21 MET cc_start: 0.7369 (mpp) cc_final: 0.6645 (mpp) REVERT: A 154 MET cc_start: 0.8036 (mpp) cc_final: 0.7604 (mpp) REVERT: A 209 LEU cc_start: 0.9507 (mt) cc_final: 0.9239 (mt) REVERT: A 213 ARG cc_start: 0.9011 (mtt180) cc_final: 0.8165 (mmt-90) REVERT: A 252 PHE cc_start: 0.9630 (t80) cc_final: 0.9100 (t80) REVERT: A 281 LEU cc_start: 0.9647 (mm) cc_final: 0.9440 (mm) REVERT: A 580 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9414 (tt) REVERT: A 691 MET cc_start: 0.9241 (mmm) cc_final: 0.8992 (mmm) REVERT: A 726 ASP cc_start: 0.9143 (t70) cc_final: 0.8791 (p0) REVERT: A 830 MET cc_start: 0.8841 (tpp) cc_final: 0.8332 (mmm) REVERT: A 913 THR cc_start: 0.9706 (p) cc_final: 0.9472 (t) REVERT: A 950 GLU cc_start: 0.9271 (tt0) cc_final: 0.8873 (mt-10) REVERT: A 972 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.8614 (ppp80) REVERT: A 998 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.8988 (p0) REVERT: C 21 MET cc_start: 0.7384 (mpp) cc_final: 0.6667 (mpp) REVERT: C 154 MET cc_start: 0.8072 (mpp) cc_final: 0.7650 (mpp) REVERT: C 213 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8021 (mmt-90) REVERT: C 252 PHE cc_start: 0.9600 (t80) cc_final: 0.8805 (t80) REVERT: C 281 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9389 (mm) REVERT: C 282 MET cc_start: 0.9568 (tpp) cc_final: 0.9031 (tpp) REVERT: C 303 PHE cc_start: 0.9305 (t80) cc_final: 0.8460 (t80) REVERT: C 482 ASP cc_start: 0.8761 (m-30) cc_final: 0.8535 (m-30) REVERT: C 565 MET cc_start: 0.8665 (tmm) cc_final: 0.8457 (tmm) REVERT: C 580 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9381 (tt) REVERT: C 691 MET cc_start: 0.9251 (mmm) cc_final: 0.8990 (mmm) REVERT: C 726 ASP cc_start: 0.9143 (t70) cc_final: 0.8789 (p0) REVERT: C 799 MET cc_start: 0.8125 (tpp) cc_final: 0.7924 (tpp) REVERT: C 830 MET cc_start: 0.8161 (tpp) cc_final: 0.7803 (tpp) REVERT: C 972 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8609 (ppp80) REVERT: C 998 ASP cc_start: 0.9269 (OUTLIER) cc_final: 0.8977 (p0) REVERT: D 21 MET cc_start: 0.7376 (mpp) cc_final: 0.6649 (mpp) REVERT: D 154 MET cc_start: 0.8070 (mpp) cc_final: 0.7644 (mpp) REVERT: D 213 ARG cc_start: 0.9045 (mtt180) cc_final: 0.8005 (mmt-90) REVERT: D 252 PHE cc_start: 0.9602 (t80) cc_final: 0.8802 (t80) REVERT: D 281 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9406 (mm) REVERT: D 303 PHE cc_start: 0.9308 (t80) cc_final: 0.8457 (t80) REVERT: D 482 ASP cc_start: 0.8805 (m-30) cc_final: 0.8529 (m-30) REVERT: D 580 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9382 (tt) REVERT: D 691 MET cc_start: 0.9249 (mmm) cc_final: 0.8986 (mmm) REVERT: D 726 ASP cc_start: 0.9143 (t70) cc_final: 0.8783 (p0) REVERT: D 830 MET cc_start: 0.9030 (tpp) cc_final: 0.8500 (mmm) REVERT: D 913 THR cc_start: 0.9698 (p) cc_final: 0.9457 (t) REVERT: D 972 ARG cc_start: 0.9359 (OUTLIER) cc_final: 0.8623 (ppp80) REVERT: D 998 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.8988 (p0) outliers start: 81 outliers final: 45 residues processed: 333 average time/residue: 0.3465 time to fit residues: 193.8784 Evaluate side-chains 311 residues out of total 3156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 429 TYR Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 800 CYS Chi-restraints excluded: chain B residue 820 CYS Chi-restraints excluded: chain B residue 949 LEU Chi-restraints excluded: chain B residue 972 ARG Chi-restraints excluded: chain B residue 998 ASP Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 800 CYS Chi-restraints excluded: chain A residue 820 CYS Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 949 LEU Chi-restraints excluded: chain A residue 972 ARG Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 395 PHE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 580 LEU Chi-restraints excluded: chain C residue 820 CYS Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 949 LEU Chi-restraints excluded: chain C residue 972 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 429 TYR Chi-restraints excluded: chain D residue 561 LEU Chi-restraints excluded: chain D residue 580 LEU Chi-restraints excluded: chain D residue 741 LEU Chi-restraints excluded: chain D residue 800 CYS Chi-restraints excluded: chain D residue 820 CYS Chi-restraints excluded: chain D residue 972 ARG Chi-restraints excluded: chain D residue 998 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3148 > 50: distance: 28 - 155: 24.935 distance: 38 - 158: 17.247 distance: 100 - 101: 5.288 distance: 100 - 103: 7.142 distance: 101 - 102: 14.229 distance: 101 - 106: 10.533 distance: 103 - 105: 9.295 distance: 106 - 107: 23.179 distance: 107 - 108: 38.843 distance: 107 - 110: 27.369 distance: 108 - 109: 36.267 distance: 108 - 113: 52.206 distance: 110 - 111: 24.059 distance: 110 - 112: 21.110 distance: 113 - 114: 55.716 distance: 114 - 115: 41.473 distance: 115 - 116: 47.897 distance: 115 - 117: 27.445 distance: 116 - 132: 29.605 distance: 117 - 118: 13.122 distance: 118 - 119: 7.355 distance: 118 - 121: 5.810 distance: 119 - 120: 17.123 distance: 119 - 124: 9.220 distance: 121 - 122: 9.036 distance: 121 - 123: 9.105 distance: 124 - 125: 22.162 distance: 125 - 126: 15.673 distance: 125 - 128: 20.397 distance: 126 - 127: 19.442 distance: 126 - 132: 15.765 distance: 128 - 129: 11.116 distance: 129 - 130: 14.228 distance: 129 - 131: 13.662 distance: 132 - 133: 35.833 distance: 133 - 134: 56.003 distance: 133 - 136: 36.835 distance: 134 - 135: 44.949 distance: 134 - 140: 62.208 distance: 136 - 137: 20.576 distance: 136 - 138: 25.311 distance: 137 - 139: 22.708 distance: 140 - 141: 47.338 distance: 140 - 146: 56.982 distance: 141 - 142: 33.161 distance: 141 - 144: 32.439 distance: 142 - 143: 11.070 distance: 142 - 147: 38.312 distance: 144 - 145: 32.797 distance: 145 - 146: 24.883 distance: 147 - 148: 6.531 distance: 148 - 149: 49.963 distance: 148 - 151: 31.910 distance: 149 - 150: 34.210 distance: 149 - 155: 46.342 distance: 151 - 152: 23.949 distance: 151 - 153: 29.207 distance: 152 - 154: 49.479 distance: 155 - 156: 31.079 distance: 156 - 157: 18.962 distance: 156 - 159: 13.903 distance: 157 - 158: 22.578 distance: 157 - 163: 22.865 distance: 159 - 160: 12.954 distance: 159 - 161: 23.633 distance: 160 - 162: 27.635 distance: 163 - 164: 27.345 distance: 164 - 165: 17.175 distance: 164 - 167: 46.552 distance: 165 - 166: 27.446 distance: 165 - 170: 16.140 distance: 167 - 168: 39.393 distance: 167 - 169: 46.770