Starting phenix.real_space_refine on Tue Aug 26 13:53:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n82_49109/08_2025/9n82_49109.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 1.337 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: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 189 5.16 5 C 23621 2.51 5 N 6439 2.21 5 O 7417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37812 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4169 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 28, 'TRANS': 487} Chain breaks: 1 Chain: "B" Number of atoms: 4115 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 4104 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 512, 4104 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 23, 'TRANS': 488} Chain breaks: 1 bond proxies already assigned to first conformer: 4173 Chain: "C" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1887 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 12, 'TRANS': 225} Chain breaks: 1 Chain: "D" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "E" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "F" Number of atoms: 5648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5648 Classifications: {'peptide': 699} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 672} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 174 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 3, 'TRANS': 20} Chain: "H" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 165 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 3, 'TRANS': 19} Chain: "I" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 790 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 776 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain: "L" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 33} Chain: "a" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4094 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "b" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4092 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 23, 'TRANS': 486} Chain breaks: 1 Chain: "c" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1876 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain breaks: 1 Chain: "d" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "e" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1628 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "f" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2069 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 10, 'TRANS': 244} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 315 " occ=0.45 ... (20 atoms not shown) pdb=" NH2BARG B 315 " occ=0.55 Time building chain proxies: 7.98, per 1000 atoms: 0.21 Number of scatterers: 37812 At special positions: 0 Unit cell: (204.085, 243.236, 178.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 146 15.00 O 7417 8.00 N 6439 7.00 C 23621 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8270 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 39 sheets defined 44.8% alpha, 19.2% beta 73 base pairs and 121 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.868A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.594A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.846A pdb=" N GLN A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 135 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.641A pdb=" N VAL A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 197 removed outlier: 3.836A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.450A pdb=" N ILE A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.712A pdb=" N ASP A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 377 through 393 removed outlier: 3.681A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 480 through 496 Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.673A pdb=" N GLN B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.706A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 198 through 216 Processing helix chain 'B' and resid 217 through 224 removed outlier: 3.749A pdb=" N ASP B 222 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 349 through 351 No H-bonds generated for 'chain 'B' and resid 349 through 351' Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.728A pdb=" N LEU B 430 " --> pdb=" O MET B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 461 Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.689A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.644A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.867A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing helix chain 'C' and resid 0 through 10 Processing helix chain 'C' and resid 52 through 62 removed outlier: 4.229A pdb=" N GLN C 56 " --> pdb=" O SER C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 86 Proline residue: C 82 - end of helix Processing helix chain 'C' and resid 127 through 170 removed outlier: 5.383A pdb=" N ARG C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 197 through 202 Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 215 through 229 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 118 through 201 removed outlier: 4.257A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 199 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 118 through 201 removed outlier: 4.285A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU E 147 " --> pdb=" O HIS E 143 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 201 " --> pdb=" O LYS E 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.819A pdb=" N LEU F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.776A pdb=" N LYS F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 removed outlier: 4.046A pdb=" N LEU F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 76 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 114 through 118 removed outlier: 4.235A pdb=" N GLY F 117 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 removed outlier: 3.522A pdb=" N ILE F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 179 through 192 Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 211 through 219 Processing helix chain 'F' and resid 220 through 228 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.516A pdb=" N PHE F 302 " --> pdb=" O TYR F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.633A pdb=" N ILE F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 381 through 391 removed outlier: 3.648A pdb=" N SER F 391 " --> pdb=" O GLU F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 424 removed outlier: 3.609A pdb=" N VAL F 414 " --> pdb=" O THR F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 685 removed outlier: 3.506A pdb=" N PHE F 685 " --> pdb=" O ARG F 681 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 715 Processing helix chain 'F' and resid 723 through 733 Processing helix chain 'F' and resid 747 through 756 removed outlier: 3.869A pdb=" N GLU F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 753 " --> pdb=" O SER F 749 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 Processing helix chain 'F' and resid 788 through 804 Processing helix chain 'F' and resid 836 through 848 removed outlier: 3.962A pdb=" N ILE F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 871 through 882 Processing helix chain 'F' and resid 891 through 901 removed outlier: 3.547A pdb=" N THR F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 910 Processing helix chain 'a' and resid 45 through 50 removed outlier: 3.720A pdb=" N GLU a 50 " --> pdb=" O ALA a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 78 Processing helix chain 'a' and resid 112 through 121 removed outlier: 3.709A pdb=" N GLN a 121 " --> pdb=" O LEU a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 135 Processing helix chain 'a' and resid 142 through 157 removed outlier: 3.715A pdb=" N VAL a 157 " --> pdb=" O LEU a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 197 removed outlier: 3.739A pdb=" N ALA a 183 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 221 removed outlier: 4.372A pdb=" N ILE a 220 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 244 removed outlier: 3.673A pdb=" N ASP a 241 " --> pdb=" O SER a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 314 No H-bonds generated for 'chain 'a' and resid 312 through 314' Processing helix chain 'a' and resid 330 through 337 Processing helix chain 'a' and resid 354 through 356 No H-bonds generated for 'chain 'a' and resid 354 through 356' Processing helix chain 'a' and resid 357 through 361 removed outlier: 3.540A pdb=" N TYR a 361 " --> pdb=" O LYS a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.678A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 480 through 496 Processing helix chain 'a' and resid 510 through 519 Processing helix chain 'a' and resid 520 through 530 Processing helix chain 'b' and resid 17 through 21 Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 97 Processing helix chain 'b' and resid 106 through 123 removed outlier: 3.528A pdb=" N ALA b 110 " --> pdb=" O ASP b 106 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE b 123 " --> pdb=" O GLN b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 158 Processing helix chain 'b' and resid 198 through 216 Processing helix chain 'b' and resid 217 through 222 Processing helix chain 'b' and resid 227 through 234 Processing helix chain 'b' and resid 306 through 308 No H-bonds generated for 'chain 'b' and resid 306 through 308' Processing helix chain 'b' and resid 324 through 332 Processing helix chain 'b' and resid 349 through 351 No H-bonds generated for 'chain 'b' and resid 349 through 351' Processing helix chain 'b' and resid 352 through 356 Processing helix chain 'b' and resid 370 through 388 Processing helix chain 'b' and resid 447 through 461 Processing helix chain 'b' and resid 478 through 482 removed outlier: 3.570A pdb=" N LYS b 481 " --> pdb=" O PRO b 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.658A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 516 Processing helix chain 'b' and resid 519 through 526 removed outlier: 3.600A pdb=" N THR b 523 " --> pdb=" O PRO b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 526 through 537 Processing helix chain 'c' and resid 1 through 11 Processing helix chain 'c' and resid 51 through 62 Processing helix chain 'c' and resid 68 through 86 Proline residue: c 82 - end of helix Processing helix chain 'c' and resid 127 through 171 removed outlier: 5.159A pdb=" N ARG c 137 " --> pdb=" O GLN c 133 " (cutoff:3.500A) Proline residue: c 138 - end of helix removed outlier: 3.596A pdb=" N GLY c 171 " --> pdb=" O TYR c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 180 removed outlier: 3.944A pdb=" N LEU c 179 " --> pdb=" O ARG c 176 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 197 Processing helix chain 'c' and resid 197 through 202 Processing helix chain 'c' and resid 207 through 214 Processing helix chain 'c' and resid 215 through 228 removed outlier: 3.599A pdb=" N MET c 219 " --> pdb=" O GLN c 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 295 through 299 removed outlier: 3.977A pdb=" N PHE c 298 " --> pdb=" O ARG c 295 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 31 Processing helix chain 'd' and resid 48 through 60 removed outlier: 3.636A pdb=" N SER d 53 " --> pdb=" O GLU d 49 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN d 54 " --> pdb=" O SER d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 75 Processing helix chain 'd' and resid 118 through 201 removed outlier: 4.099A pdb=" N VAL d 122 " --> pdb=" O ASN d 118 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL d 183 " --> pdb=" O ARG d 179 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU d 199 " --> pdb=" O HIS d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 60 Processing helix chain 'e' and resid 62 through 75 Processing helix chain 'e' and resid 118 through 201 removed outlier: 4.004A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA e 139 " --> pdb=" O ALA e 135 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS e 164 " --> pdb=" O GLY e 160 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA e 171 " --> pdb=" O SER e 167 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU e 173 " --> pdb=" O LYS e 169 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG e 179 " --> pdb=" O ASP e 175 " (cutoff:3.500A) Processing helix chain 'f' and resid 674 through 686 Processing helix chain 'f' and resid 706 through 715 Processing helix chain 'f' and resid 723 through 733 Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.880A pdb=" N ARG f 756 " --> pdb=" O GLU f 752 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 Processing helix chain 'f' and resid 788 through 804 Processing helix chain 'f' and resid 836 through 848 removed outlier: 3.943A pdb=" N ILE f 840 " --> pdb=" O THR f 836 " (cutoff:3.500A) Processing helix chain 'f' and resid 871 through 882 Processing helix chain 'f' and resid 891 through 899 removed outlier: 3.572A pdb=" N THR f 895 " --> pdb=" O GLU f 891 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP f 899 " --> pdb=" O THR f 895 " (cutoff:3.500A) Processing helix chain 'f' and resid 905 through 910 removed outlier: 3.950A pdb=" N GLN f 908 " --> pdb=" O GLU f 905 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU f 910 " --> pdb=" O ASN f 907 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 109 removed outlier: 4.971A pdb=" N VAL A 104 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 87 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 108 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU A 83 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG A 35 " --> pdb=" O HIS A 163 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ARG A 165 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N SER A 37 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N MET A 167 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 39 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 169 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 41 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 168 " --> pdb=" O MET A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.678A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 431 " --> pdb=" O GLN A 416 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 345 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'A' and resid 296 through 304 removed outlier: 3.545A pdb=" N GLU B 292 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR B 295 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 420 removed outlier: 6.770A pdb=" N GLU A 419 " --> pdb=" O VAL A 427 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.276A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 133 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 247 through 253 removed outlier: 3.915A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLY B 344 " --> pdb=" O THR B 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 464 through 466 Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 18 removed outlier: 6.068A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 12.648A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.555A pdb=" N SER E 105 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N PHE E 97 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER E 110 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE E 95 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR E 94 " --> pdb=" O SER E 89 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 89 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL E 83 " --> pdb=" O ASN E 100 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 9 Processing sheet with id=AB6, first strand: chain 'D' and resid 85 through 89 Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AB8, first strand: chain 'F' and resid 250 through 253 removed outlier: 7.204A pdb=" N LEU F 250 " --> pdb=" O TRP F 447 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LYS F 449 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA F 252 " --> pdb=" O LYS F 449 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 287 through 291 removed outlier: 4.585A pdb=" N ALA F 334 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 287 through 291 removed outlier: 6.468A pdb=" N ILE F 325 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET F 371 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE F 327 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N VAL F 369 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP F 329 " --> pdb=" O PHE F 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 688 through 689 removed outlier: 7.019A pdb=" N GLU F 663 " --> pdb=" O CYS F 699 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE F 701 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS F 665 " --> pdb=" O ILE F 701 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 851 through 852 removed outlier: 6.138A pdb=" N THR F 817 " --> pdb=" O HIS F 862 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE F 864 " --> pdb=" O THR F 817 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 102 through 109 removed outlier: 5.089A pdb=" N VAL a 104 " --> pdb=" O PHE a 87 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE a 87 " --> pdb=" O VAL a 104 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU a 108 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU a 83 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP a 36 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA a 84 " --> pdb=" O ASP a 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU a 38 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL a 86 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N PHE a 40 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TYR a 88 " --> pdb=" O PHE a 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL a 42 " --> pdb=" O TYR a 88 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N MET a 203 " --> pdb=" O ILE a 166 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU a 168 " --> pdb=" O MET a 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.522A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY a 349 " --> pdb=" O LEU a 397 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ARG a 399 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LEU a 347 " --> pdb=" O ARG a 399 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR a 401 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU a 345 " --> pdb=" O THR a 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 286 through 289 removed outlier: 3.535A pdb=" N ASP b 319 " --> pdb=" O TYR b 316 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 296 through 304 removed outlier: 3.620A pdb=" N PHE a 303 " --> pdb=" O GLN b 290 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN b 290 " --> pdb=" O PHE a 303 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 326 through 329 Processing sheet with id=AC9, first strand: chain 'a' and resid 375 through 376 Processing sheet with id=AD1, first strand: chain 'a' and resid 419 through 420 Processing sheet with id=AD2, first strand: chain 'b' and resid 77 through 84 removed outlier: 5.334A pdb=" N VAL b 79 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU b 58 " --> pdb=" O VAL b 79 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU b 83 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE b 54 " --> pdb=" O LEU b 83 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP b 15 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'b' and resid 247 through 253 removed outlier: 4.098A pdb=" N LEU b 257 " --> pdb=" O ILE b 253 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU b 268 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASN b 359 " --> pdb=" O LEU b 268 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.537A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG b 394 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL b 342 " --> pdb=" O ARG b 394 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ALA b 396 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE b 340 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 464 through 467 Processing sheet with id=AD5, first strand: chain 'c' and resid 14 through 17 removed outlier: 3.524A pdb=" N MET c 124 " --> pdb=" O HIS c 46 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N ASP c 50 " --> pdb=" O ASN c 120 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N ASN c 120 " --> pdb=" O ASP c 50 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 2 through 8 Processing sheet with id=AD7, first strand: chain 'd' and resid 83 through 89 removed outlier: 4.163A pdb=" N VAL d 83 " --> pdb=" O ASN d 100 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS d 99 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ARG d 107 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU d 101 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER d 105 " --> pdb=" O LEU d 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 2 through 8 Processing sheet with id=AD9, first strand: chain 'e' and resid 83 through 89 removed outlier: 4.425A pdb=" N VAL e 83 " --> pdb=" O ASN e 100 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS e 99 " --> pdb=" O ARG e 107 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG e 107 " --> pdb=" O LYS e 99 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'f' and resid 688 through 689 removed outlier: 3.600A pdb=" N PHE f 664 " --> pdb=" O TYR f 688 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N GLU f 663 " --> pdb=" O CYS f 699 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE f 701 " --> pdb=" O GLU f 663 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS f 665 " --> pdb=" O ILE f 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'f' and resid 720 through 721 removed outlier: 6.908A pdb=" N VAL f 720 " --> pdb=" O ILE f 744 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'f' and resid 851 through 852 removed outlier: 6.136A pdb=" N THR f 817 " --> pdb=" O HIS f 862 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE f 864 " --> pdb=" O THR f 817 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR f 819 " --> pdb=" O ILE f 864 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL f 863 " --> pdb=" O LEU f 889 " (cutoff:3.500A) 1767 hydrogen bonds defined for protein. 5035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 177 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 121 stacking parallelities Total time for adding SS restraints: 7.27 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11664 1.34 - 1.46: 6496 1.46 - 1.58: 20124 1.58 - 1.70: 287 1.70 - 1.82: 300 Bond restraints: 38871 Sorted by residual: bond pdb=" C CYS F 225 " pdb=" N ARG F 226 " ideal model delta sigma weight residual 1.334 1.374 -0.040 1.41e-02 5.03e+03 7.97e+00 bond pdb=" O3' DC I 54 " pdb=" P DT I 55 " ideal model delta sigma weight residual 1.607 1.574 0.033 1.50e-02 4.44e+03 4.77e+00 bond pdb=" O3' DA K 13 " pdb=" P DG K 14 " ideal model delta sigma weight residual 1.607 1.640 -0.033 1.50e-02 4.44e+03 4.73e+00 bond pdb=" C GLY d 79 " pdb=" N PRO d 80 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.28e-02 6.10e+03 3.79e+00 bond pdb=" N MET e 1 " pdb=" CA MET e 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 38866 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 52308 2.04 - 4.09: 718 4.09 - 6.13: 32 6.13 - 8.18: 1 8.18 - 10.22: 4 Bond angle restraints: 53063 Sorted by residual: angle pdb=" CB MET a 498 " pdb=" CG MET a 498 " pdb=" SD MET a 498 " ideal model delta sigma weight residual 112.70 122.92 -10.22 3.00e+00 1.11e-01 1.16e+01 angle pdb=" CB MET e 1 " pdb=" CG MET e 1 " pdb=" SD MET e 1 " ideal model delta sigma weight residual 112.70 122.47 -9.77 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CA ARG D 150 " pdb=" CB ARG D 150 " pdb=" CG ARG D 150 " ideal model delta sigma weight residual 114.10 120.32 -6.22 2.00e+00 2.50e-01 9.69e+00 angle pdb=" C1' AMP F1001 " pdb=" C2' AMP F1001 " pdb=" C3' AMP F1001 " ideal model delta sigma weight residual 111.00 102.17 8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" O CYS F 225 " pdb=" C CYS F 225 " pdb=" N ARG F 226 " ideal model delta sigma weight residual 122.27 125.69 -3.42 1.23e+00 6.61e-01 7.75e+00 ... (remaining 53058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19304 18.00 - 35.99: 2780 35.99 - 53.99: 1036 53.99 - 71.98: 221 71.98 - 89.98: 51 Dihedral angle restraints: 23392 sinusoidal: 10697 harmonic: 12695 Sorted by residual: dihedral pdb=" CA TYR D 84 " pdb=" C TYR D 84 " pdb=" N THR D 85 " pdb=" CA THR D 85 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" C4' AMP F1001 " pdb=" C5' AMP F1001 " pdb=" O5' AMP F1001 " pdb=" P AMP F1001 " ideal model delta sinusoidal sigma weight residual -180.00 -120.09 -59.91 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" C2' AMP F1001 " pdb=" C1' AMP F1001 " pdb=" N9 AMP F1001 " pdb=" C4 AMP F1001 " ideal model delta sinusoidal sigma weight residual 91.55 33.19 58.36 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 23389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 4840 0.046 - 0.092: 774 0.092 - 0.138: 281 0.138 - 0.184: 7 0.184 - 0.230: 1 Chirality restraints: 5903 Sorted by residual: chirality pdb=" C2' AMP F1001 " pdb=" C1' AMP F1001 " pdb=" C3' AMP F1001 " pdb=" O2' AMP F1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA ILE F 796 " pdb=" N ILE F 796 " pdb=" C ILE F 796 " pdb=" CB ILE F 796 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE B 24 " pdb=" N ILE B 24 " pdb=" C ILE B 24 " pdb=" CB ILE B 24 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 5900 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 796 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ILE F 796 " -0.045 2.00e-02 2.50e+03 pdb=" O ILE F 796 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA F 797 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 185 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" CG ASN D 185 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN D 185 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN D 185 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG c 151 " 0.141 9.50e-02 1.11e+02 6.31e-02 2.63e+00 pdb=" NE ARG c 151 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG c 151 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG c 151 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG c 151 " 0.003 2.00e-02 2.50e+03 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 12009 2.84 - 3.36: 34977 3.36 - 3.87: 62046 3.87 - 4.39: 69733 4.39 - 4.90: 116640 Nonbonded interactions: 295405 Sorted by model distance: nonbonded pdb=" O GLU D 51 " pdb=" OE2 GLU D 55 " model vdw 2.326 3.040 nonbonded pdb=" O SER D 50 " pdb=" OE1 GLN D 54 " model vdw 2.344 3.040 nonbonded pdb=" OG SER D 53 " pdb=" OE1 GLN D 54 " model vdw 2.345 3.040 nonbonded pdb=" O THR c 66 " pdb=" OG1 THR c 66 " model vdw 2.426 3.040 nonbonded pdb=" O SER e 76 " pdb=" OG SER e 76 " model vdw 2.433 3.040 ... (remaining 295400 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 or resid 33 through 538)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 6 through 168 or resid 196 through 314 or resid 316 throug \ h 542)) selection = (chain 'b' and (resid 6 through 314 or resid 316 through 542)) } ncs_group { reference = (chain 'C' and (resid 0 through 228 or resid 293 through 299)) selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'G' and resid 180 through 202) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 34.430 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.003 0.044 38872 Z= 0.124 Angle : 0.537 10.221 53063 Z= 0.294 Chirality : 0.039 0.230 5903 Planarity : 0.003 0.063 6303 Dihedral : 19.177 89.977 15122 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.16 % Allowed : 23.72 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.13), residues: 4287 helix: 2.58 (0.13), residues: 1740 sheet: 0.68 (0.20), residues: 719 loop : -0.22 (0.15), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 368 TYR 0.018 0.001 TYR F 823 PHE 0.026 0.001 PHE D 180 TRP 0.021 0.001 TRP F 805 HIS 0.010 0.001 HIS f 745 Details of bonding type rmsd covalent geometry : bond 0.00262 (38871) covalent geometry : angle 0.53695 (53063) hydrogen bonds : bond 0.11263 ( 1930) hydrogen bonds : angle 5.09326 ( 5389) Misc. bond : bond 0.03821 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 547 time to evaluate : 1.003 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: 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: D 138 GLN cc_start: 0.8811 (tt0) cc_final: 0.8331 (tp-100) REVERT: D 177 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.8409 (t80) REVERT: E 57 ASP cc_start: 0.9207 (m-30) cc_final: 0.8828 (p0) REVERT: E 176 LEU cc_start: 0.9438 (tp) cc_final: 0.8986 (tp) REVERT: d 8 ILE cc_start: 0.8754 (pt) cc_final: 0.8372 (mp) REVERT: d 19 PHE cc_start: 0.8340 (m-80) cc_final: 0.8060 (m-80) REVERT: d 128 CYS cc_start: 0.8445 (m) cc_final: 0.7566 (t) REVERT: f 805 TRP cc_start: 0.7588 (m-10) cc_final: 0.7308 (m-10) REVERT: f 812 MET cc_start: 0.8337 (ptt) cc_final: 0.8043 (ppp) outliers start: 45 outliers final: 15 residues processed: 585 average time/residue: 0.2142 time to fit residues: 200.0960 Evaluate side-chains 380 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 364 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain D residue 9 HIS Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain b residue 245 ILE Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 71 ARG Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain e residue 106 PHE Chi-restraints excluded: chain e residue 192 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN A 326 GLN B 45 GLN B 120 HIS D 195 HIS D 200 ASN E 40 HIS F 783 ASN a 416 GLN ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 HIS ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 137 ASN e 145 GLN f 869 HIS ** f 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.087494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.058137 restraints weight = 228595.053| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.78 r_work: 0.2874 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38872 Z= 0.147 Angle : 0.599 12.712 53063 Z= 0.310 Chirality : 0.041 0.343 5903 Planarity : 0.004 0.050 6303 Dihedral : 16.130 72.254 6284 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.88 % Allowed : 23.23 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.13), residues: 4287 helix: 2.54 (0.13), residues: 1743 sheet: 0.89 (0.19), residues: 689 loop : -0.16 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG e 150 TYR 0.014 0.001 TYR f 698 PHE 0.026 0.001 PHE d 162 TRP 0.024 0.001 TRP f 738 HIS 0.007 0.001 HIS F 848 Details of bonding type rmsd covalent geometry : bond 0.00338 (38871) covalent geometry : angle 0.59911 (53063) hydrogen bonds : bond 0.03923 ( 1930) hydrogen bonds : angle 4.38660 ( 5389) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 372 time to evaluate : 1.181 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8393 (mmp-170) cc_final: 0.8048 (mmm160) REVERT: A 252 ARG cc_start: 0.7531 (tpt170) cc_final: 0.7263 (ttt-90) REVERT: B 210 MET cc_start: 0.8831 (tmm) cc_final: 0.8573 (ppp) REVERT: B 212 MET cc_start: 0.9294 (mmm) cc_final: 0.9094 (mmm) REVERT: C 47 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8358 (tt0) REVERT: C 86 ASP cc_start: 0.8359 (t0) cc_final: 0.7432 (t0) REVERT: C 142 MET cc_start: 0.9241 (mtp) cc_final: 0.9019 (mtp) REVERT: D 138 GLN cc_start: 0.9540 (tt0) cc_final: 0.9009 (tp-100) REVERT: D 177 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8918 (t80) REVERT: E 57 ASP cc_start: 0.9190 (m-30) cc_final: 0.8774 (p0) REVERT: E 134 ILE cc_start: 0.9605 (mm) cc_final: 0.9335 (mm) REVERT: E 150 ARG cc_start: 0.9281 (tpt90) cc_final: 0.9078 (tpt90) REVERT: F 88 MET cc_start: 0.9338 (mmm) cc_final: 0.8936 (mmm) REVERT: F 812 MET cc_start: 0.8345 (ptt) cc_final: 0.7503 (ptt) REVERT: a 498 MET cc_start: 0.8950 (mmm) cc_final: 0.8098 (tpp) REVERT: c 59 LYS cc_start: 0.8944 (tppt) cc_final: 0.8731 (tppt) REVERT: c 174 LEU cc_start: 0.7444 (mp) cc_final: 0.6839 (mt) REVERT: d 32 PHE cc_start: 0.8717 (p90) cc_final: 0.8488 (p90) REVERT: d 61 MET cc_start: 0.8319 (tpt) cc_final: 0.7297 (tmm) REVERT: d 162 PHE cc_start: 0.9624 (OUTLIER) cc_final: 0.9374 (t80) REVERT: d 177 TYR cc_start: 0.9235 (m-80) cc_final: 0.8800 (m-80) REVERT: e 191 ILE cc_start: 0.9396 (tt) cc_final: 0.9100 (pt) REVERT: e 192 ARG cc_start: 0.9585 (OUTLIER) cc_final: 0.9246 (ptp-110) REVERT: f 677 ASP cc_start: 0.9662 (t0) cc_final: 0.9427 (t0) REVERT: f 719 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: f 805 TRP cc_start: 0.7950 (m-10) cc_final: 0.7368 (m-10) REVERT: f 812 MET cc_start: 0.8631 (ptt) cc_final: 0.8221 (ptp) outliers start: 112 outliers final: 45 residues processed: 465 average time/residue: 0.2036 time to fit residues: 156.6579 Evaluate side-chains 371 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 321 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 474 GLU Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain a residue 79 ASP Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 504 VAL Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 162 PHE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 801 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 434 optimal weight: 30.0000 chunk 111 optimal weight: 0.1980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 GLN E 118 ASN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 148 ASN F 783 ASN F 904 GLN b 43 GLN b 66 ASN b 432 GLN ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 908 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.053977 restraints weight = 181646.309| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.54 r_work: 0.2744 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 38872 Z= 0.296 Angle : 0.650 10.560 53063 Z= 0.339 Chirality : 0.042 0.198 5903 Planarity : 0.004 0.063 6303 Dihedral : 16.641 76.653 6269 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.76 % Allowed : 22.41 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.13), residues: 4287 helix: 2.22 (0.12), residues: 1738 sheet: 0.59 (0.19), residues: 738 loop : -0.21 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG d 150 TYR 0.015 0.002 TYR D 84 PHE 0.026 0.002 PHE E 19 TRP 0.017 0.002 TRP E 43 HIS 0.006 0.001 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00678 (38871) covalent geometry : angle 0.65024 (53063) hydrogen bonds : bond 0.04566 ( 1930) hydrogen bonds : angle 4.56350 ( 5389) Misc. bond : bond 0.00094 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 317 time to evaluate : 1.274 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: symmetry clash revert: symmetry clash REVERT: A 185 ARG cc_start: 0.8486 (mmp-170) cc_final: 0.8237 (mmm160) REVERT: A 498 MET cc_start: 0.8451 (tpp) cc_final: 0.8069 (tpp) REVERT: B 84 MET cc_start: 0.9384 (ptp) cc_final: 0.8621 (pmm) REVERT: B 120 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8650 (p90) REVERT: B 210 MET cc_start: 0.9050 (tmm) cc_final: 0.8544 (ppp) REVERT: B 212 MET cc_start: 0.9491 (mmm) cc_final: 0.9233 (mmm) REVERT: C 216 ASP cc_start: 0.9213 (p0) cc_final: 0.8939 (p0) REVERT: D 138 GLN cc_start: 0.9560 (tt0) cc_final: 0.9068 (tp-100) REVERT: D 177 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.9146 (t80) REVERT: D 179 ARG cc_start: 0.9427 (OUTLIER) cc_final: 0.9052 (ttm170) REVERT: E 57 ASP cc_start: 0.9219 (m-30) cc_final: 0.8877 (p0) REVERT: F 88 MET cc_start: 0.9449 (mmm) cc_final: 0.9208 (mmm) REVERT: F 102 ASP cc_start: 0.9535 (m-30) cc_final: 0.8974 (p0) REVERT: F 812 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7955 (ptt) REVERT: F 841 LYS cc_start: 0.9575 (OUTLIER) cc_final: 0.9145 (mttt) REVERT: a 135 MET cc_start: 0.8723 (mmt) cc_final: 0.8494 (mmt) REVERT: a 498 MET cc_start: 0.9100 (mmm) cc_final: 0.8263 (tpp) REVERT: b 87 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8035 (t70) REVERT: c 174 LEU cc_start: 0.7381 (mp) cc_final: 0.6732 (mt) REVERT: d 32 PHE cc_start: 0.9074 (p90) cc_final: 0.8779 (p90) REVERT: d 61 MET cc_start: 0.8610 (tpt) cc_final: 0.7572 (tmm) REVERT: d 129 TYR cc_start: 0.9090 (t80) cc_final: 0.8810 (t80) REVERT: d 162 PHE cc_start: 0.9637 (OUTLIER) cc_final: 0.9424 (t80) REVERT: d 177 TYR cc_start: 0.9396 (m-80) cc_final: 0.8888 (m-80) REVERT: e 10 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8896 (tp) REVERT: e 192 ARG cc_start: 0.9630 (OUTLIER) cc_final: 0.9187 (ptp-110) REVERT: f 719 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: f 812 MET cc_start: 0.8827 (ptt) cc_final: 0.8389 (ptp) REVERT: f 823 TYR cc_start: 0.8169 (m-80) cc_final: 0.7952 (m-80) outliers start: 146 outliers final: 78 residues processed: 441 average time/residue: 0.2040 time to fit residues: 150.0286 Evaluate side-chains 375 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 245 LYS Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 13 CYS Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 HIS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 202 THR Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain F residue 841 LYS Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 296 VAL Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 504 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 273 LYS Chi-restraints excluded: chain b residue 275 THR Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 195 ILE Chi-restraints excluded: chain d residue 44 THR Chi-restraints excluded: chain d residue 85 THR Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 162 PHE Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 103 ASP Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 801 TYR Chi-restraints excluded: chain f residue 806 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 401 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 419 optimal weight: 0.7980 chunk 354 optimal weight: 2.9990 chunk 437 optimal weight: 20.0000 chunk 137 optimal weight: 2.9990 chunk 386 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS A 326 GLN ** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN F 338 ASN F 783 ASN a 326 GLN ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.084755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055126 restraints weight = 185454.057| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.69 r_work: 0.2787 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38872 Z= 0.152 Angle : 0.567 12.250 53063 Z= 0.296 Chirality : 0.040 0.160 5903 Planarity : 0.004 0.041 6303 Dihedral : 16.508 75.744 6264 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.68 % Allowed : 23.57 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.13), residues: 4287 helix: 2.39 (0.13), residues: 1739 sheet: 0.63 (0.19), residues: 731 loop : -0.19 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 151 TYR 0.011 0.001 TYR D 84 PHE 0.024 0.001 PHE A 216 TRP 0.009 0.001 TRP C 15 HIS 0.014 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00346 (38871) covalent geometry : angle 0.56746 (53063) hydrogen bonds : bond 0.03691 ( 1930) hydrogen bonds : angle 4.30928 ( 5389) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 318 time to evaluate : 1.098 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: A 48 MET cc_start: 0.8637 (mmt) cc_final: 0.7778 (mmm) REVERT: A 185 ARG cc_start: 0.8474 (mmp-170) cc_final: 0.8220 (mmm160) REVERT: A 498 MET cc_start: 0.8485 (tpp) cc_final: 0.8111 (tpp) REVERT: B 84 MET cc_start: 0.9420 (ptp) cc_final: 0.8662 (pmm) REVERT: B 212 MET cc_start: 0.9535 (mmm) cc_final: 0.9330 (mmm) REVERT: C 180 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8357 (tptt) REVERT: D 138 GLN cc_start: 0.9577 (tt0) cc_final: 0.9104 (tp-100) REVERT: D 177 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.9037 (t80) REVERT: D 179 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.9027 (ttm170) REVERT: F 88 MET cc_start: 0.9409 (mmm) cc_final: 0.9175 (mmm) REVERT: F 102 ASP cc_start: 0.9528 (m-30) cc_final: 0.8963 (p0) REVERT: F 127 MET cc_start: 0.9080 (mmp) cc_final: 0.8416 (mmm) REVERT: F 812 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7874 (ptt) REVERT: a 135 MET cc_start: 0.8767 (mmt) cc_final: 0.8514 (mmt) REVERT: a 311 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8782 (mm) REVERT: a 498 MET cc_start: 0.9107 (mmm) cc_final: 0.8377 (tpp) REVERT: b 87 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.7988 (t0) REVERT: c 174 LEU cc_start: 0.7290 (mp) cc_final: 0.6642 (mt) REVERT: d 32 PHE cc_start: 0.9069 (p90) cc_final: 0.8757 (p90) REVERT: d 61 MET cc_start: 0.8701 (tpt) cc_final: 0.7670 (tmm) REVERT: d 177 TYR cc_start: 0.9331 (m-80) cc_final: 0.8875 (m-80) REVERT: d 179 ARG cc_start: 0.9543 (OUTLIER) cc_final: 0.8888 (ttm110) REVERT: e 10 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8810 (tp) REVERT: e 59 MET cc_start: 0.9380 (tpp) cc_final: 0.8951 (tpp) REVERT: e 192 ARG cc_start: 0.9623 (OUTLIER) cc_final: 0.8886 (ptp-170) REVERT: f 677 ASP cc_start: 0.9671 (OUTLIER) cc_final: 0.9432 (t0) REVERT: f 719 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.8320 (m-30) REVERT: f 812 MET cc_start: 0.8862 (ptt) cc_final: 0.8435 (ptp) REVERT: f 823 TYR cc_start: 0.8234 (m-80) cc_final: 0.7944 (m-80) outliers start: 104 outliers final: 61 residues processed: 407 average time/residue: 0.2028 time to fit residues: 136.6056 Evaluate side-chains 365 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 311 LEU Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 354 VAL Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 504 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 272 VAL Chi-restraints excluded: chain b residue 273 LYS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 495 LEU Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 195 ILE Chi-restraints excluded: chain d residue 7 ARG Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 103 ASP Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 677 ASP Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 801 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 106 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 234 optimal weight: 0.6980 chunk 290 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 326 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.084539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.055070 restraints weight = 179903.250| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.60 r_work: 0.2789 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38872 Z= 0.153 Angle : 0.557 12.102 53063 Z= 0.290 Chirality : 0.040 0.195 5903 Planarity : 0.004 0.041 6303 Dihedral : 16.489 75.593 6264 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.09 % Allowed : 23.26 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.13), residues: 4287 helix: 2.38 (0.13), residues: 1739 sheet: 0.63 (0.19), residues: 731 loop : -0.20 (0.15), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 151 TYR 0.011 0.001 TYR c 167 PHE 0.027 0.001 PHE A 216 TRP 0.007 0.001 TRP C 15 HIS 0.006 0.001 HIS e 40 Details of bonding type rmsd covalent geometry : bond 0.00347 (38871) covalent geometry : angle 0.55712 (53063) hydrogen bonds : bond 0.03616 ( 1930) hydrogen bonds : angle 4.27374 ( 5389) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 300 time to evaluate : 1.400 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: A 215 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8859 (tt) REVERT: A 249 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9033 (tptm) REVERT: A 498 MET cc_start: 0.8532 (tpp) cc_final: 0.8171 (tpp) REVERT: B 84 MET cc_start: 0.9408 (ptp) cc_final: 0.8619 (pmm) REVERT: B 212 MET cc_start: 0.9537 (mmm) cc_final: 0.9317 (mmm) REVERT: D 138 GLN cc_start: 0.9571 (tt0) cc_final: 0.9083 (tp-100) REVERT: D 177 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.9021 (t80) REVERT: D 179 ARG cc_start: 0.9431 (OUTLIER) cc_final: 0.9092 (ttm170) REVERT: E 57 ASP cc_start: 0.8933 (m-30) cc_final: 0.8592 (p0) REVERT: F 102 ASP cc_start: 0.9517 (m-30) cc_final: 0.8975 (p0) REVERT: F 812 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7825 (ptt) REVERT: a 135 MET cc_start: 0.8769 (mmt) cc_final: 0.8521 (mmt) REVERT: a 161 MET cc_start: 0.8907 (mtm) cc_final: 0.8689 (mtm) REVERT: a 453 MET cc_start: 0.8994 (tpp) cc_final: 0.8790 (mmp) REVERT: a 498 MET cc_start: 0.9123 (mmm) cc_final: 0.8404 (tpp) REVERT: b 87 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.7965 (t70) REVERT: c 174 LEU cc_start: 0.7198 (mp) cc_final: 0.6465 (mt) REVERT: d 61 MET cc_start: 0.8674 (tpt) cc_final: 0.7690 (tmm) REVERT: d 177 TYR cc_start: 0.9328 (m-80) cc_final: 0.8803 (m-80) REVERT: e 10 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8841 (tp) REVERT: e 192 ARG cc_start: 0.9609 (OUTLIER) cc_final: 0.8865 (ptp-170) REVERT: f 677 ASP cc_start: 0.9672 (t0) cc_final: 0.9422 (t0) REVERT: f 719 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: f 812 MET cc_start: 0.8852 (ptt) cc_final: 0.8426 (ptp) REVERT: f 823 TYR cc_start: 0.8179 (m-80) cc_final: 0.7894 (m-80) outliers start: 120 outliers final: 76 residues processed: 400 average time/residue: 0.2028 time to fit residues: 134.9715 Evaluate side-chains 369 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 746 MET Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain a residue 79 ASP Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 354 VAL Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 504 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 272 VAL Chi-restraints excluded: chain b residue 273 LYS Chi-restraints excluded: chain b residue 275 THR Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 495 LEU Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain c residue 80 LEU Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 195 ILE Chi-restraints excluded: chain c residue 203 SER Chi-restraints excluded: chain d residue 7 ARG Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 103 ASP Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 801 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 269 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 106 optimal weight: 0.0050 chunk 89 optimal weight: 4.9990 chunk 165 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 326 GLN C 48 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 176 HIS a 489 ASN b 119 GLN ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.085103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.055250 restraints weight = 225183.968| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.85 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38872 Z= 0.123 Angle : 0.556 11.510 53063 Z= 0.288 Chirality : 0.039 0.221 5903 Planarity : 0.003 0.041 6303 Dihedral : 16.439 75.268 6264 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.62 % Allowed : 23.64 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.13), residues: 4287 helix: 2.41 (0.13), residues: 1742 sheet: 0.62 (0.19), residues: 736 loop : -0.17 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 151 TYR 0.014 0.001 TYR d 129 PHE 0.029 0.001 PHE d 32 TRP 0.007 0.001 TRP D 43 HIS 0.005 0.001 HIS e 40 Details of bonding type rmsd covalent geometry : bond 0.00274 (38871) covalent geometry : angle 0.55636 (53063) hydrogen bonds : bond 0.03424 ( 1930) hydrogen bonds : angle 4.21600 ( 5389) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 310 time to evaluate : 1.204 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: A 96 SER cc_start: 0.9248 (m) cc_final: 0.9015 (p) REVERT: A 185 ARG cc_start: 0.8469 (mmp-170) cc_final: 0.8249 (mmm160) REVERT: A 215 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8813 (tt) REVERT: A 249 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8624 (tptp) REVERT: A 498 MET cc_start: 0.8208 (tpp) cc_final: 0.7867 (tpp) REVERT: B 84 MET cc_start: 0.9261 (ptp) cc_final: 0.8584 (pmm) REVERT: B 212 MET cc_start: 0.9585 (mmm) cc_final: 0.9373 (mmm) REVERT: B 389 MET cc_start: 0.9074 (mtp) cc_final: 0.8663 (mtp) REVERT: D 1 MET cc_start: 0.8745 (tpp) cc_final: 0.8468 (tpt) REVERT: D 138 GLN cc_start: 0.9361 (tt0) cc_final: 0.8871 (tp-100) REVERT: D 177 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8646 (t80) REVERT: D 179 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8809 (ttm170) REVERT: E 57 ASP cc_start: 0.8784 (m-30) cc_final: 0.8489 (p0) REVERT: F 88 MET cc_start: 0.8489 (mmm) cc_final: 0.8211 (mmm) REVERT: F 102 ASP cc_start: 0.9431 (m-30) cc_final: 0.8985 (p0) REVERT: F 127 MET cc_start: 0.8547 (mmp) cc_final: 0.7837 (mmm) REVERT: F 289 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7896 (mttp) REVERT: F 354 MET cc_start: 0.4173 (mmm) cc_final: 0.3850 (mmm) REVERT: F 812 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7694 (ptt) REVERT: H 183 GLU cc_start: 0.8167 (tp30) cc_final: 0.7944 (tp30) REVERT: a 135 MET cc_start: 0.8685 (mmt) cc_final: 0.8481 (mmt) REVERT: a 161 MET cc_start: 0.8682 (mtm) cc_final: 0.8456 (mtm) REVERT: a 310 LEU cc_start: 0.9200 (tt) cc_final: 0.8953 (mm) REVERT: a 498 MET cc_start: 0.8628 (mmm) cc_final: 0.8089 (tpp) REVERT: b 87 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8034 (t70) REVERT: c 174 LEU cc_start: 0.7287 (mp) cc_final: 0.6589 (mt) REVERT: d 61 MET cc_start: 0.8467 (tpt) cc_final: 0.7667 (tmm) REVERT: d 177 TYR cc_start: 0.8987 (m-80) cc_final: 0.8377 (m-80) REVERT: d 179 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8522 (ttm110) REVERT: e 10 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8817 (tp) REVERT: e 192 ARG cc_start: 0.9542 (OUTLIER) cc_final: 0.8833 (ptp-170) REVERT: f 677 ASP cc_start: 0.9485 (t0) cc_final: 0.9277 (t0) REVERT: f 719 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: f 812 MET cc_start: 0.8761 (ptt) cc_final: 0.8362 (ptp) REVERT: f 823 TYR cc_start: 0.8144 (m-80) cc_final: 0.7891 (m-80) outliers start: 102 outliers final: 71 residues processed: 395 average time/residue: 0.2159 time to fit residues: 140.3137 Evaluate side-chains 368 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 286 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 746 MET Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain a residue 79 ASP Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 296 VAL Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 504 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 272 VAL Chi-restraints excluded: chain b residue 273 LYS Chi-restraints excluded: chain b residue 305 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 103 ASP Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 801 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 439 random chunks: chunk 368 optimal weight: 0.9980 chunk 241 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 339 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN F 783 ASN b 43 GLN b 298 ASN ** c 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.054792 restraints weight = 195341.910| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.89 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38872 Z= 0.170 Angle : 0.571 10.751 53063 Z= 0.296 Chirality : 0.040 0.280 5903 Planarity : 0.003 0.041 6303 Dihedral : 16.494 76.136 6264 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.06 % Allowed : 23.46 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.13), residues: 4287 helix: 2.37 (0.13), residues: 1740 sheet: 0.60 (0.19), residues: 725 loop : -0.17 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 151 TYR 0.017 0.001 TYR F 801 PHE 0.028 0.001 PHE A 216 TRP 0.009 0.001 TRP E 155 HIS 0.005 0.001 HIS F 316 Details of bonding type rmsd covalent geometry : bond 0.00390 (38871) covalent geometry : angle 0.57149 (53063) hydrogen bonds : bond 0.03614 ( 1930) hydrogen bonds : angle 4.27092 ( 5389) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 292 time to evaluate : 1.193 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: A 96 SER cc_start: 0.9274 (m) cc_final: 0.9057 (p) REVERT: A 185 ARG cc_start: 0.8451 (mmp-170) cc_final: 0.8245 (mmm160) REVERT: A 215 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8843 (tt) REVERT: A 249 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8776 (tptm) REVERT: A 446 MET cc_start: 0.8953 (mmp) cc_final: 0.8615 (mmt) REVERT: A 498 MET cc_start: 0.8257 (tpp) cc_final: 0.7919 (tpp) REVERT: B 84 MET cc_start: 0.9310 (ptp) cc_final: 0.8562 (pmm) REVERT: B 212 MET cc_start: 0.9502 (mmm) cc_final: 0.9287 (mmm) REVERT: C 85 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9217 (ttmm) REVERT: D 138 GLN cc_start: 0.9428 (tt0) cc_final: 0.8902 (tp-100) REVERT: D 177 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8755 (t80) REVERT: D 179 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8877 (ttm170) REVERT: E 57 ASP cc_start: 0.8871 (m-30) cc_final: 0.8574 (p0) REVERT: F 102 ASP cc_start: 0.9489 (m-30) cc_final: 0.9023 (p0) REVERT: F 289 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7816 (mttp) REVERT: F 812 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7659 (ptt) REVERT: H 194 LYS cc_start: 0.9034 (ptpt) cc_final: 0.8657 (pttm) REVERT: a 132 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: a 310 LEU cc_start: 0.9159 (tt) cc_final: 0.8913 (mm) REVERT: a 498 MET cc_start: 0.8669 (mmm) cc_final: 0.8192 (tpp) REVERT: b 87 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8029 (t70) REVERT: c 111 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: c 174 LEU cc_start: 0.7282 (mp) cc_final: 0.6560 (mt) REVERT: d 61 MET cc_start: 0.8474 (tpt) cc_final: 0.7747 (tmm) REVERT: d 177 TYR cc_start: 0.9064 (m-80) cc_final: 0.8458 (m-80) REVERT: e 10 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8816 (tp) REVERT: e 192 ARG cc_start: 0.9565 (OUTLIER) cc_final: 0.8821 (ptp-170) REVERT: f 677 ASP cc_start: 0.9573 (t0) cc_final: 0.9333 (t0) REVERT: f 719 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: f 812 MET cc_start: 0.8783 (ptt) cc_final: 0.8369 (ptp) REVERT: f 823 TYR cc_start: 0.7981 (m-80) cc_final: 0.7754 (m-80) REVERT: f 845 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9276 (mm) outliers start: 119 outliers final: 82 residues processed: 394 average time/residue: 0.1923 time to fit residues: 126.3309 Evaluate side-chains 372 residues out of total 3886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 277 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 133 GLN Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 128 CYS Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 179 ARG Chi-restraints excluded: chain E residue 16 ILE Chi-restraints excluded: chain E residue 143 HIS Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 165 ASP Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 746 MET Chi-restraints excluded: chain F residue 759 ASP Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 783 ASN Chi-restraints excluded: chain F residue 812 MET Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 79 ASP Chi-restraints excluded: chain a residue 95 ASN Chi-restraints excluded: chain a residue 132 GLN Chi-restraints excluded: chain a residue 219 ASP Chi-restraints excluded: chain a residue 223 ILE Chi-restraints excluded: chain a residue 296 VAL Chi-restraints excluded: chain a residue 316 THR Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 420 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain b residue 87 ASP Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 272 VAL Chi-restraints excluded: chain b residue 273 LYS Chi-restraints excluded: chain b residue 275 THR Chi-restraints excluded: chain b residue 305 VAL Chi-restraints excluded: chain b residue 339 CYS Chi-restraints excluded: chain b residue 470 THR Chi-restraints excluded: chain b residue 515 MET Chi-restraints excluded: chain b residue 533 ILE Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 77 ASP Chi-restraints excluded: chain c residue 99 CYS Chi-restraints excluded: chain c residue 111 GLU Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain d residue 92 SER Chi-restraints excluded: chain d residue 111 PHE Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 103 ASP Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain e residue 192 ARG Chi-restraints excluded: chain f residue 719 ASP Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 801 TYR Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2816 > 50: distance: 33 - 228: 7.213 distance: 36 - 225: 20.920 distance: 49 - 213: 31.845 distance: 52 - 210: 15.377 distance: 121 - 221: 18.830 distance: 124 - 218: 25.581 distance: 138 - 207: 33.413 distance: 140 - 148: 21.566 distance: 141 - 204: 26.391 distance: 148 - 149: 42.008 distance: 149 - 150: 6.362 distance: 150 - 151: 46.839 distance: 152 - 153: 27.620 distance: 152 - 154: 38.349 distance: 153 - 155: 12.352 distance: 156 - 157: 41.723 distance: 157 - 158: 20.984 distance: 157 - 160: 21.742 distance: 158 - 165: 65.686 distance: 160 - 161: 14.951 distance: 161 - 162: 8.582 distance: 162 - 163: 14.309 distance: 163 - 164: 10.408 distance: 165 - 166: 36.253 distance: 166 - 167: 56.000 distance: 166 - 169: 56.361 distance: 167 - 175: 57.194 distance: 169 - 170: 11.378 distance: 170 - 171: 26.987 distance: 170 - 172: 12.531 distance: 171 - 173: 3.814 distance: 173 - 174: 37.070 distance: 175 - 176: 40.828 distance: 176 - 177: 55.235 distance: 176 - 179: 29.289 distance: 177 - 183: 5.672 distance: 179 - 180: 39.091 distance: 180 - 181: 27.323 distance: 180 - 182: 39.780 distance: 183 - 184: 41.637 distance: 184 - 185: 20.279 distance: 184 - 187: 20.630 distance: 185 - 186: 39.744 distance: 185 - 195: 43.428 distance: 187 - 188: 27.069 distance: 188 - 189: 15.850 distance: 188 - 190: 42.096 distance: 189 - 191: 24.961 distance: 190 - 192: 6.621 distance: 191 - 193: 39.618 distance: 192 - 193: 17.172 distance: 195 - 196: 19.891 distance: 196 - 197: 4.144 distance: 197 - 198: 21.830 distance: 197 - 204: 25.482 distance: 199 - 200: 25.970 distance: 200 - 201: 22.279 distance: 201 - 202: 15.983 distance: 201 - 203: 27.470 distance: 204 - 205: 33.182 distance: 205 - 206: 16.381 distance: 205 - 208: 21.547 distance: 206 - 207: 5.748 distance: 206 - 210: 19.820 distance: 208 - 209: 16.804 distance: 210 - 211: 13.460 distance: 211 - 212: 19.593 distance: 211 - 214: 26.157 distance: 212 - 213: 14.199 distance: 212 - 218: 52.624 distance: 214 - 215: 16.371 distance: 215 - 216: 35.203 distance: 215 - 217: 49.643 distance: 218 - 219: 16.318 distance: 219 - 220: 12.983 distance: 219 - 222: 29.282 distance: 220 - 221: 22.126 distance: 220 - 225: 9.422 distance: 222 - 223: 18.908 distance: 222 - 224: 39.193 distance: 225 - 226: 6.012 distance: 226 - 227: 7.414 distance: 226 - 229: 8.581 distance: 227 - 228: 16.655 distance: 227 - 237: 10.476 distance: 229 - 230: 5.753 distance: 230 - 231: 10.010 distance: 230 - 232: 6.900 distance: 231 - 233: 3.739 distance: 232 - 234: 7.734 distance: 233 - 235: 4.590 distance: 234 - 235: 7.118 distance: 235 - 236: 19.972