Starting phenix.real_space_refine on Mon Jul 6 19:54:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.map" model { file = "/net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n83_49110/07_2026/9n83_49110.cif" } resolution = 3.1 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= 0.007 sd= 1.367 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: 6 Type Number sf(0) Gaussians P 146 5.49 5 Mg 1 5.21 5 S 202 5.16 5 C 24459 2.51 5 N 6660 2.21 5 O 7656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39124 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: 6959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 866, 6959 Classifications: {'peptide': 866} Link IDs: {'PTRANS': 37, 'TRANS': 828} Chain breaks: 1 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: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 700 Classifications: {'DNA': 34} 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: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {' MG': 1, 'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG B 315 " occ=0.40 ... (20 atoms not shown) pdb=" NH2BARG B 315 " occ=0.60 Time building chain proxies: 8.99, per 1000 atoms: 0.23 Number of scatterers: 39124 At special positions: 0 Unit cell: (204.918, 244.069, 178.262, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 202 16.00 P 146 15.00 Mg 1 11.99 O 7656 8.00 N 6660 7.00 C 24459 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: 3.46 Conformation dependent library (CDL) restraints added in 1.8 seconds 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8574 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 43 sheets defined 44.6% alpha, 19.6% beta 73 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 5.00 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 4.382A pdb=" N SER A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 78 removed outlier: 3.720A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.618A pdb=" N ILE A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 136 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.966A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 Processing helix chain 'A' and resid 216 through 221 removed outlier: 4.377A pdb=" N ILE A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.754A 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: 3.801A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.707A pdb=" N LYS A 443 " --> pdb=" O ALA A 440 " (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 17 through 22 removed outlier: 3.995A pdb=" N SER B 21 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.790A pdb=" N GLN B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 96 removed outlier: 3.702A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 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: 3.757A pdb=" N ASP B 222 " --> pdb=" O ASP B 219 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.639A pdb=" N LYS B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) 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 removed outlier: 3.707A pdb=" N PHE B 355 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 356 " --> pdb=" O ARG B 353 " (cutoff:3.500A) No H-bonds generated for '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: 3.585A pdb=" N LYS B 481 " --> pdb=" O PRO B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.728A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 removed outlier: 3.734A pdb=" N TRP B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.868A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.093A 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 53 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 170 removed outlier: 5.493A 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 176 through 180 removed outlier: 3.769A pdb=" N LEU C 179 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 180 " --> pdb=" O ASP C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 197 through 203 Processing helix chain 'C' and resid 207 through 213 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: 4.293A pdb=" N VAL D 122 " --> pdb=" O ASN D 118 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS D 197 " --> pdb=" O SER D 193 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 199 " --> pdb=" O HIS D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 29 No H-bonds generated for 'chain 'E' and resid 27 through 29' Processing helix chain 'E' and resid 49 through 59 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 118 through 201 removed outlier: 4.227A pdb=" N VAL E 122 " --> pdb=" O ASN E 118 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 170 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU E 173 " --> pdb=" O LYS E 169 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR E 174 " --> pdb=" O GLU E 170 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.922A pdb=" N LEU F 19 " --> pdb=" O PRO F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 54 removed outlier: 3.577A pdb=" N LYS F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 72 removed outlier: 4.095A 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: 4.213A pdb=" N GLY F 117 " --> pdb=" O THR F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 144 through 161 Processing helix chain 'F' and resid 163 through 177 removed outlier: 3.870A pdb=" N ILE F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) 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 removed outlier: 3.548A pdb=" N VAL F 217 " --> pdb=" O GLU F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 228 Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 311 through 316 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 390 removed outlier: 3.878A pdb=" N SER F 390 " --> pdb=" O TYR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 424 removed outlier: 3.652A pdb=" N VAL F 414 " --> pdb=" O THR F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 455 Processing helix chain 'F' and resid 473 through 477 removed outlier: 3.576A pdb=" N GLY F 477 " --> pdb=" O GLY F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 523 Processing helix chain 'F' and resid 550 through 554 Processing helix chain 'F' and resid 589 through 593 removed outlier: 3.559A pdb=" N CYS F 593 " --> pdb=" O TRP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 595 through 606 removed outlier: 4.134A pdb=" N ALA F 606 " --> pdb=" O LEU F 602 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 684 Processing helix chain 'F' and resid 706 through 716 removed outlier: 3.545A pdb=" N ASN F 716 " --> pdb=" O ILE F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 722 through 733 removed outlier: 4.474A pdb=" N LEU F 726 " --> pdb=" O LYS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 756 removed outlier: 4.221A pdb=" N GLU F 752 " --> pdb=" O PRO F 748 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS F 753 " --> pdb=" O SER F 749 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 781 removed outlier: 3.545A pdb=" N ILE F 781 " --> pdb=" O VAL F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 804 Processing helix chain 'F' and resid 805 through 808 Processing helix chain 'F' and resid 836 through 849 removed outlier: 3.878A 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: 4.934A pdb=" N ASP F 899 " --> pdb=" O THR F 895 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS F 900 " --> pdb=" O ASP F 896 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 50 removed outlier: 4.075A 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 120 removed outlier: 3.543A pdb=" N ILE a 116 " --> pdb=" O GLY a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 123 No H-bonds generated for 'chain 'a' and resid 121 through 123' Processing helix chain 'a' and resid 124 through 135 Processing helix chain 'a' and resid 142 through 157 removed outlier: 3.744A pdb=" N VAL a 157 " --> pdb=" O LEU a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 197 removed outlier: 3.810A pdb=" N ALA a 183 " --> pdb=" O ASP a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 216 through 221 removed outlier: 4.392A pdb=" N ILE a 220 " --> pdb=" O PHE a 216 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 244 removed outlier: 3.865A 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 357 through 361 removed outlier: 3.564A pdb=" N HIS a 360 " --> pdb=" O LYS a 357 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR a 361 " --> pdb=" O LYS a 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 357 through 361' Processing helix chain 'a' and resid 377 through 393 removed outlier: 3.716A pdb=" N LEU a 381 " --> pdb=" O GLY a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 439 through 443 removed outlier: 3.710A pdb=" N LYS a 443 " --> pdb=" O ALA a 440 " (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 22 removed outlier: 3.812A pdb=" N SER b 21 " --> pdb=" O GLY b 17 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN b 22 " --> pdb=" O PHE b 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 17 through 22' Processing helix chain 'b' and resid 29 through 48 Processing helix chain 'b' and resid 87 through 97 removed outlier: 3.544A pdb=" N LEU b 91 " --> pdb=" O ASP b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 123 removed outlier: 4.210A 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 218 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: 3.654A pdb=" N LYS b 481 " --> pdb=" O PRO b 478 " (cutoff:3.500A) Processing helix chain 'b' and resid 484 through 500 removed outlier: 3.682A pdb=" N GLN b 488 " --> pdb=" O ASN b 484 " (cutoff:3.500A) Processing helix chain 'b' and resid 509 through 517 Processing helix chain 'b' and resid 519 through 526 removed outlier: 3.723A 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 50 through 62 removed outlier: 3.501A pdb=" N VAL c 54 " --> pdb=" O ASP c 50 " (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: 5.343A 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 176 through 180 removed outlier: 3.905A 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 Processing helix chain 'd' and resid 27 through 31 Processing helix chain 'd' and resid 48 through 60 removed outlier: 3.613A pdb=" N ILE d 52 " --> pdb=" O SER d 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER d 53 " --> pdb=" O GLU d 49 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLN d 54 " --> pdb=" O SER d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 75 removed outlier: 3.898A pdb=" N LEU d 75 " --> pdb=" O ARG d 71 " (cutoff:3.500A) Processing helix chain 'd' and resid 118 through 201 removed outlier: 4.358A pdb=" N VAL d 122 " --> pdb=" O ASN d 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL d 183 " --> pdb=" O ARG d 179 " (cutoff:3.500A) removed outlier: 3.763A 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: 4.078A pdb=" N VAL e 122 " --> pdb=" O ASN e 118 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS e 164 " --> pdb=" O GLY e 160 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA e 171 " --> pdb=" O SER e 167 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU e 173 " --> pdb=" O LYS e 169 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR e 174 " --> pdb=" O GLU e 170 " (cutoff:3.500A) removed outlier: 3.605A 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 removed outlier: 3.579A pdb=" N LEU f 727 " --> pdb=" O PRO f 723 " (cutoff:3.500A) Processing helix chain 'f' and resid 747 through 758 removed outlier: 3.537A pdb=" N ARG f 756 " --> pdb=" O GLU f 752 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU f 757 " --> pdb=" O HIS f 753 " (cutoff:3.500A) Processing helix chain 'f' and resid 770 through 781 removed outlier: 4.021A pdb=" N ILE f 781 " --> pdb=" O VAL f 777 " (cutoff:3.500A) Processing helix chain 'f' and resid 788 through 804 Processing helix chain 'f' and resid 836 through 848 removed outlier: 3.961A 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: 3.911A pdb=" N ASP f 899 " --> pdb=" O THR f 895 " (cutoff:3.500A) Processing helix chain 'f' and resid 906 through 910 removed outlier: 3.611A 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: 5.209A pdb=" N VAL A 104 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE A 87 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 108 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU A 83 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP A 36 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA A 84 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG A 35 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS A 163 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 43 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N PHE A 199 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET A 203 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.965A 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: 3.601A pdb=" N SER A 257 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 431 " --> pdb=" O GLN A 416 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR A 401 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU A 345 " --> pdb=" O THR A 401 " (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: 3.599A pdb=" N GLU B 292 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.622A 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: 6.595A 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 81 removed outlier: 6.301A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA B 9 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG B 130 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN B 162 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE B 132 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N PHE B 164 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 6.428A 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: 3.788A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLN B 360 " --> pdb=" O GLN B 423 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN B 423 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 10.305A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N PHE B 340 " --> pdb=" O PRO B 248 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG B 250 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 342 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR B 252 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 7.632A 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: 6.479A pdb=" N GLN C 48 " --> pdb=" O HIS C 122 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N HIS C 122 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 11.592A pdb=" N ASP C 50 " --> pdb=" O ASN C 120 " (cutoff:3.500A) removed outlier: 12.674A pdb=" N ASN C 120 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL C 100 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 66 removed outlier: 5.035A pdb=" N SER E 105 " --> pdb=" O LEU E 101 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU E 101 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG E 107 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LYS E 99 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.993A 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 8 Processing sheet with id=AB6, first strand: chain 'D' and resid 2 through 8 removed outlier: 3.600A pdb=" N THR D 44 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU D 114 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 84 through 89 Processing sheet with id=AB8, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AB9, first strand: chain 'F' and resid 252 through 253 removed outlier: 6.299A pdb=" N ALA F 252 " --> pdb=" O LYS F 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 287 through 291 removed outlier: 4.283A pdb=" N ALA F 334 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 287 through 291 removed outlier: 6.697A pdb=" N ILE F 325 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET F 371 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE F 327 " --> pdb=" O VAL F 369 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL F 369 " --> pdb=" O ILE F 327 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP F 329 " --> pdb=" O PHE F 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 527 through 528 removed outlier: 11.637A pdb=" N ASP F 463 " --> pdb=" O ALA F 488 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA F 488 " --> pdb=" O ASP F 463 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU F 484 " --> pdb=" O VAL F 467 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLY F 469 " --> pdb=" O HIS F 482 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N HIS F 482 " --> pdb=" O GLY F 469 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TRP F 471 " --> pdb=" O MET F 480 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET F 480 " --> pdb=" O TRP F 471 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE F 483 " --> pdb=" O ARG F 505 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG F 505 " --> pdb=" O PHE F 483 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N CYS F 485 " --> pdb=" O LEU F 503 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 527 through 528 removed outlier: 4.290A pdb=" N ILE F 556 " --> pdb=" O ARG F 585 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS F 583 " --> pdb=" O GLN F 558 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS F 560 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ILE F 581 " --> pdb=" O LYS F 560 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 563 through 566 removed outlier: 3.907A pdb=" N GLU F 563 " --> pdb=" O ARG F 577 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 688 through 689 removed outlier: 3.885A pdb=" N CYS F 699 " --> pdb=" O GLU F 663 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS F 665 " --> pdb=" O CYS F 699 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL F 700 " --> pdb=" O VAL F 721 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 851 through 853 removed outlier: 6.332A pdb=" N VAL F 818 " --> pdb=" O VAL F 853 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR F 817 " --> pdb=" O HIS F 862 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE F 864 " --> pdb=" O THR F 817 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR F 819 " --> pdb=" O ILE F 864 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL F 863 " --> pdb=" O LEU F 889 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'a' and resid 102 through 109 removed outlier: 5.060A pdb=" N VAL a 104 " --> pdb=" O PHE a 87 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N PHE a 87 " --> pdb=" O VAL a 104 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU a 108 " --> pdb=" O LEU a 83 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU a 83 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASP a 36 " --> pdb=" O LEU a 82 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ALA a 84 " --> pdb=" O ASP a 36 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU a 38 " --> pdb=" O ALA a 84 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL a 86 " --> pdb=" O LEU a 38 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N PHE a 40 " --> pdb=" O VAL a 86 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TYR a 88 " --> pdb=" O PHE a 40 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL a 42 " --> pdb=" O TYR a 88 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG a 35 " --> pdb=" O HIS a 163 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ARG a 165 " --> pdb=" O ARG a 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER a 37 " --> pdb=" O ARG a 165 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N MET a 167 " --> pdb=" O SER a 37 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE a 39 " --> pdb=" O MET a 167 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N PHE a 169 " --> pdb=" O ILE a 39 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU a 41 " --> pdb=" O PHE a 169 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N PHE a 199 " --> pdb=" O SER a 162 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS a 164 " --> pdb=" O PHE a 199 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASP a 201 " --> pdb=" O LYS a 164 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE a 166 " --> pdb=" O ASP a 201 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N MET a 203 " --> pdb=" O ILE a 166 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU a 168 " --> pdb=" O MET a 203 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'a' and resid 257 through 262 removed outlier: 3.632A pdb=" N SER a 257 " --> pdb=" O ILE a 273 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE a 410 " --> pdb=" O LEU a 437 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL a 394 " --> pdb=" O PRO a 415 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY a 349 " --> pdb=" O LEU a 397 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG a 399 " --> pdb=" O LEU a 347 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU a 347 " --> pdb=" O ARG a 399 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR a 401 " --> pdb=" O LEU a 345 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU a 345 " --> pdb=" O THR a 401 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 286 through 289 removed outlier: 3.564A pdb=" N ASP b 319 " --> pdb=" O TYR b 316 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 297 through 302 removed outlier: 4.350A pdb=" N TYR b 295 " --> pdb=" O VAL b 305 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 326 through 329 Processing sheet with id=AD4, first strand: chain 'a' and resid 375 through 376 Processing sheet with id=AD5, first strand: chain 'a' and resid 419 through 420 Processing sheet with id=AD6, first strand: chain 'b' and resid 77 through 84 removed outlier: 5.237A pdb=" N VAL b 79 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU b 58 " --> pdb=" O VAL b 79 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU b 83 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE b 54 " --> pdb=" O LEU b 83 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL b 10 " --> pdb=" O ALA b 55 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL b 57 " --> pdb=" O VAL b 10 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU b 12 " --> pdb=" O VAL b 57 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N PHE b 59 " --> pdb=" O LEU b 12 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET b 14 " --> pdb=" O PHE b 59 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 15 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG b 130 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N GLN b 162 " --> pdb=" O ARG b 130 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE b 132 " --> pdb=" O GLN b 162 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N PHE b 164 " --> pdb=" O ILE b 132 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE b 134 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N TYR b 225 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE b 163 " --> pdb=" O TYR b 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 247 through 253 removed outlier: 4.019A pdb=" N LEU b 257 " --> pdb=" O ILE b 253 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL b 361 " --> pdb=" O SER b 266 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU b 268 " --> pdb=" O ASN b 359 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N ASN b 359 " --> pdb=" O LEU b 268 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N GLN b 360 " --> pdb=" O GLN b 423 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN b 423 " --> pdb=" O GLN b 360 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA b 366 " --> pdb=" O GLU b 417 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N GLU b 417 " --> pdb=" O ALA b 366 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N MET b 389 " --> pdb=" O PRO b 410 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG b 394 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL b 342 " --> pdb=" O ARG b 394 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ALA b 396 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N PHE b 340 " --> pdb=" O ALA b 396 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N PHE b 340 " --> pdb=" O PRO b 248 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ARG b 250 " --> pdb=" O PHE b 340 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL b 342 " --> pdb=" O ARG b 250 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR b 252 " --> pdb=" O VAL b 342 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N GLY b 344 " --> pdb=" O THR b 252 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'b' and resid 464 through 467 Processing sheet with id=AD9, first strand: chain 'c' and resid 14 through 17 removed outlier: 6.825A pdb=" N GLN c 48 " --> pdb=" O HIS c 122 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N HIS c 122 " --> pdb=" O GLN c 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 65 through 66 removed outlier: 3.534A pdb=" N SER e 105 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ARG e 107 " --> pdb=" O LYS e 99 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS e 99 " --> pdb=" O ARG e 107 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL e 83 " --> pdb=" O ASN e 100 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'd' and resid 2 through 8 Processing sheet with id=AE3, first strand: chain 'd' and resid 83 through 89 removed outlier: 4.251A pdb=" N VAL d 83 " --> pdb=" O ASN d 100 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS d 99 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG d 107 " --> pdb=" O LYS d 99 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU d 101 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N SER d 105 " --> pdb=" O LEU d 101 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'e' and resid 2 through 9 Processing sheet with id=AE5, first strand: chain 'f' and resid 663 through 664 removed outlier: 3.944A pdb=" N PHE f 664 " --> pdb=" O TYR f 688 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'f' and resid 700 through 701 removed outlier: 6.308A pdb=" N VAL f 700 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS f 745 " --> pdb=" O VAL f 720 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'f' and resid 851 through 852 removed outlier: 6.073A pdb=" N THR f 817 " --> pdb=" O HIS f 862 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE f 864 " --> pdb=" O THR f 817 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR f 819 " --> pdb=" O ILE f 864 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL f 863 " --> pdb=" O LEU f 889 " (cutoff:3.500A) 1823 hydrogen bonds defined for protein. 5185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 177 hydrogen bonds 354 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11677 1.33 - 1.45: 6430 1.45 - 1.57: 21500 1.57 - 1.69: 288 1.69 - 1.81: 320 Bond restraints: 40215 Sorted by residual: bond pdb=" C3' DT K 29 " pdb=" C2' DT K 29 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.74e+00 bond pdb=" C3' DG K 26 " pdb=" C2' DG K 26 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DA L 9 " pdb=" C2' DA L 9 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 bond pdb=" C3' DG L 21 " pdb=" C2' DG L 21 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.54e+00 bond pdb=" C3' DC K 3 " pdb=" C2' DC K 3 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 ... (remaining 40210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 53695 1.66 - 3.32: 1034 3.32 - 4.99: 131 4.99 - 6.65: 12 6.65 - 8.31: 3 Bond angle restraints: 54875 Sorted by residual: angle pdb=" N3 DT J 67 " pdb=" C4 DT J 67 " pdb=" O4 DT J 67 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT J 40 " pdb=" C4 DT J 40 " pdb=" O4 DT J 40 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 44 " pdb=" C4 DT I 44 " pdb=" O4 DT I 44 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT L 22 " pdb=" C4 DT L 22 " pdb=" O4 DT L 22 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 36 " pdb=" C4 DT J 36 " pdb=" O4 DT J 36 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 54870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.65: 21740 27.65 - 55.31: 2260 55.31 - 82.96: 196 82.96 - 110.62: 16 110.62 - 138.27: 1 Dihedral angle restraints: 24213 sinusoidal: 11040 harmonic: 13173 Sorted by residual: dihedral pdb=" C2' AMP L1001 " pdb=" C1' AMP L1001 " pdb=" N9 AMP L1001 " pdb=" C4 AMP L1001 " ideal model delta sinusoidal sigma weight residual 91.55 -46.72 138.27 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" C4' AMP L1001 " pdb=" C5' AMP L1001 " pdb=" O5' AMP L1001 " pdb=" P AMP L1001 " ideal model delta sinusoidal sigma weight residual 180.00 91.20 88.80 1 2.00e+01 2.50e-03 2.35e+01 dihedral pdb=" CA ASP F 350 " pdb=" C ASP F 350 " pdb=" N ILE F 351 " pdb=" CA ILE F 351 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 24210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4817 0.044 - 0.087: 787 0.087 - 0.131: 347 0.131 - 0.175: 141 0.175 - 0.218: 4 Chirality restraints: 6096 Sorted by residual: chirality pdb=" C2' AMP L1001 " pdb=" C1' AMP L1001 " pdb=" C3' AMP L1001 " pdb=" O2' AMP L1001 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C3' DT J 67 " pdb=" C4' DT J 67 " pdb=" O3' DT J 67 " pdb=" C2' DT J 67 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" C3' DG I 42 " pdb=" C4' DG I 42 " pdb=" O3' DG I 42 " pdb=" C2' DG I 42 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 6093 not shown) Planarity restraints: 6532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 805 " 0.022 2.00e-02 2.50e+03 1.68e-02 7.04e+00 pdb=" CG TRP F 805 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP F 805 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP F 805 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 805 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 805 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 805 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 805 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 805 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 805 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 103 " -0.016 2.00e-02 2.50e+03 1.81e-02 6.52e+00 pdb=" CG TYR A 103 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 103 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 103 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 103 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 103 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 103 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 131 " 0.017 2.00e-02 2.50e+03 1.88e-02 6.20e+00 pdb=" CG PHE A 131 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 131 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 131 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 131 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 131 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 131 " 0.005 2.00e-02 2.50e+03 ... (remaining 6529 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 11367 2.82 - 3.34: 35349 3.34 - 3.86: 63105 3.86 - 4.38: 71960 4.38 - 4.90: 121495 Nonbonded interactions: 303276 Sorted by model distance: nonbonded pdb=" O SER d 76 " pdb=" OG SER d 76 " model vdw 2.303 3.040 nonbonded pdb=" O SER e 76 " pdb=" OG SER e 76 " model vdw 2.360 3.040 nonbonded pdb=" O THR e 133 " pdb=" OD1 ASN e 137 " model vdw 2.387 3.040 nonbonded pdb=" O LEU c 112 " pdb=" OG SER c 113 " model vdw 2.404 3.040 nonbonded pdb=" O ASP B 309 " pdb=" OD1 ASP B 309 " model vdw 2.414 3.040 ... (remaining 303271 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=0.40 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: 11.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.160 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 40216 Z= 0.254 Angle : 0.554 8.310 54875 Z= 0.360 Chirality : 0.044 0.218 6096 Planarity : 0.004 0.066 6532 Dihedral : 19.488 138.272 15639 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.26 % Allowed : 25.84 % Favored : 71.90 % 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 are not related in a simple way. whole: 1.41 (0.13), residues: 4454 helix: 2.52 (0.13), residues: 1736 sheet: 0.59 (0.19), residues: 738 loop : -0.36 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 150 TYR 0.044 0.001 TYR A 103 PHE 0.042 0.001 PHE A 131 TRP 0.046 0.001 TRP F 805 HIS 0.008 0.001 HIS F 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.25 (40215) covalent geometry : angle 0.55435 / 0.36 (54875) hydrogen bonds : bond 0.11229 / 7.31 ( 1968) hydrogen bonds : angle 5.10507 / 3.63 ( 5539) Misc. bond : bond 0.09037 / 4.76 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 787 time to evaluate : 1.530 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: B 154 LEU cc_start: 0.8267 (mm) cc_final: 0.7960 (mt) REVERT: B 452 ASN cc_start: 0.8402 (m-40) cc_final: 0.8196 (m110) REVERT: C 5 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 71 ARG cc_start: 0.9211 (ttm110) cc_final: 0.8971 (ttm110) REVERT: D 154 ASP cc_start: 0.8605 (m-30) cc_final: 0.8352 (m-30) REVERT: D 194 LEU cc_start: 0.8842 (tp) cc_final: 0.8584 (tp) REVERT: F 108 LYS cc_start: 0.8953 (ttpt) cc_final: 0.8452 (tptt) REVERT: F 774 LEU cc_start: 0.8608 (tp) cc_final: 0.7887 (tt) REVERT: H 180 CYS cc_start: 0.6933 (t) cc_final: 0.6529 (t) REVERT: b 20 MET cc_start: 0.6253 (mtm) cc_final: 0.4280 (ttm) REVERT: b 40 MET cc_start: 0.8794 (mtt) cc_final: 0.8577 (mtm) REVERT: b 388 ASP cc_start: 0.8332 (t0) cc_final: 0.7944 (t0) REVERT: d 96 PHE cc_start: 0.8356 (p90) cc_final: 0.7809 (p90) REVERT: e 58 ASP cc_start: 0.8837 (m-30) cc_final: 0.7460 (m-30) REVERT: f 678 LEU cc_start: 0.9094 (mt) cc_final: 0.8821 (mt) outliers start: 91 outliers final: 44 residues processed: 855 average time/residue: 0.2746 time to fit residues: 369.9072 Evaluate side-chains 461 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 417 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 841 LYS Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 162 SER Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain b residue 13 CYS Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 86 PHE Chi-restraints excluded: chain d residue 128 CYS Chi-restraints excluded: chain d residue 143 HIS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 154 ASP Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 715 SER Chi-restraints excluded: chain f residue 749 SER Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 800 GLU Chi-restraints excluded: chain f residue 901 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN B 119 GLN B 256 ASN B 496 HIS C 89 HIS D 137 ASN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 HIS E 145 GLN F 139 GLN F 173 GLN F 183 GLN F 301 GLN a 65 GLN d 21 GLN d 159 GLN d 195 HIS e 21 GLN e 54 GLN e 159 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062329 restraints weight = 183520.385| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.35 r_work: 0.2800 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 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 = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 40216 Z= 0.171 Angle : 0.647 11.390 54875 Z= 0.347 Chirality : 0.042 0.280 6096 Planarity : 0.005 0.066 6532 Dihedral : 16.261 132.023 6508 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.02 % Allowed : 25.40 % Favored : 70.59 % 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 are not related in a simple way. whole: 1.36 (0.13), residues: 4454 helix: 2.37 (0.12), residues: 1759 sheet: 0.74 (0.19), residues: 736 loop : -0.39 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 230 TYR 0.029 0.001 TYR E 66 PHE 0.045 0.002 PHE E 180 TRP 0.026 0.001 TRP F 805 HIS 0.009 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (40215) covalent geometry : angle 0.64663 / 0.35 (54875) hydrogen bonds : bond 0.04915 / 3.26 ( 1968) hydrogen bonds : angle 4.59678 / 3.26 ( 5539) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 447 time to evaluate : 1.568 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: A 336 GLU cc_start: 0.8634 (tp30) cc_final: 0.8415 (tp30) REVERT: A 419 GLU cc_start: 0.8690 (pt0) cc_final: 0.8352 (pt0) REVERT: A 420 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (mt) REVERT: A 453 MET cc_start: 0.8721 (mmm) cc_final: 0.8499 (mmm) REVERT: B 288 ASP cc_start: 0.8684 (t70) cc_final: 0.8370 (t0) REVERT: C 187 ASN cc_start: 0.9479 (m-40) cc_final: 0.8962 (m-40) REVERT: C 195 ILE cc_start: 0.9527 (tp) cc_final: 0.9287 (pt) REVERT: D 59 MET cc_start: 0.7365 (ppp) cc_final: 0.7001 (ppp) REVERT: D 150 ARG cc_start: 0.9056 (tmm-80) cc_final: 0.8537 (tmm-80) REVERT: D 162 PHE cc_start: 0.9435 (OUTLIER) cc_final: 0.9208 (t80) REVERT: D 177 TYR cc_start: 0.9013 (m-80) cc_final: 0.8678 (m-80) REVERT: E 130 CYS cc_start: 0.9480 (m) cc_final: 0.9264 (p) REVERT: E 150 ARG cc_start: 0.8636 (tmm-80) cc_final: 0.8076 (tmm-80) REVERT: F 108 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8060 (tptt) REVERT: F 286 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8900 (t0) REVERT: F 354 MET cc_start: 0.6164 (tpt) cc_final: 0.5459 (tpt) REVERT: F 728 GLU cc_start: 0.9131 (mp0) cc_final: 0.8804 (mt-10) REVERT: F 778 PHE cc_start: 0.9343 (m-80) cc_final: 0.8927 (m-80) REVERT: F 910 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8119 (mt) REVERT: G 191 LYS cc_start: 0.9169 (mttp) cc_final: 0.8935 (mttp) REVERT: a 158 GLN cc_start: 0.8858 (mp10) cc_final: 0.8656 (mp10) REVERT: a 199 PHE cc_start: 0.8584 (t80) cc_final: 0.8234 (t80) REVERT: b 13 CYS cc_start: 0.8980 (t) cc_final: 0.8727 (m) REVERT: b 14 MET cc_start: 0.8655 (ttt) cc_final: 0.8282 (tpp) REVERT: b 20 MET cc_start: 0.6405 (mtm) cc_final: 0.3976 (ttm) REVERT: b 127 PHE cc_start: 0.7829 (m-10) cc_final: 0.7580 (m-80) REVERT: b 292 GLU cc_start: 0.9064 (tt0) cc_final: 0.8537 (tp30) REVERT: c 42 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8520 (mp10) REVERT: c 215 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8525 (mm110) REVERT: d 18 HIS cc_start: 0.8264 (m170) cc_final: 0.7002 (m170) REVERT: d 21 GLN cc_start: 0.8906 (tt0) cc_final: 0.8683 (tm-30) REVERT: d 57 ASP cc_start: 0.9511 (t0) cc_final: 0.9303 (m-30) REVERT: d 61 MET cc_start: 0.7123 (ttp) cc_final: 0.6482 (tmm) REVERT: d 138 GLN cc_start: 0.9461 (tp40) cc_final: 0.8811 (tp-100) REVERT: e 21 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8221 (pp30) REVERT: e 125 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8868 (tm-30) REVERT: e 153 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8955 (tmm160) REVERT: f 812 MET cc_start: 0.8622 (ppp) cc_final: 0.8183 (ppp) outliers start: 162 outliers final: 69 residues processed: 582 average time/residue: 0.2555 time to fit residues: 240.6595 Evaluate side-chains 452 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 375 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 685 PHE Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 841 LYS Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain F residue 910 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 329 LEU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 215 GLN Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 158 VAL Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 191 ILE Chi-restraints excluded: chain e residue 21 GLN Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 439 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 389 optimal weight: 0.6980 chunk 411 optimal weight: 4.9990 chunk 201 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 421 optimal weight: 6.9990 chunk 342 optimal weight: 8.9990 chunk 374 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 89 HIS a 293 ASN a 416 GLN b 414 HIS e 21 GLN ** f 862 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.094746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061802 restraints weight = 173399.635| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.08 r_work: 0.2811 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 40216 Z= 0.152 Angle : 0.599 13.967 54875 Z= 0.320 Chirality : 0.041 0.321 6096 Planarity : 0.004 0.053 6532 Dihedral : 16.361 131.018 6476 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.45 % Allowed : 24.26 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4454 helix: 2.35 (0.12), residues: 1744 sheet: 0.74 (0.19), residues: 735 loop : -0.38 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 71 TYR 0.020 0.001 TYR d 129 PHE 0.038 0.001 PHE e 180 TRP 0.034 0.001 TRP f 805 HIS 0.013 0.001 HIS d 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (40215) covalent geometry : angle 0.59941 / 0.32 (54875) hydrogen bonds : bond 0.04546 / 3.02 ( 1968) hydrogen bonds : angle 4.49021 / 3.17 ( 5539) Misc. bond : bond 0.00113 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 404 time to evaluate : 1.579 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: A 336 GLU cc_start: 0.8672 (tp30) cc_final: 0.8419 (tp30) REVERT: A 421 ASP cc_start: 0.8192 (t0) cc_final: 0.7968 (t0) REVERT: A 453 MET cc_start: 0.8779 (mmm) cc_final: 0.8476 (mmm) REVERT: B 14 MET cc_start: 0.8381 (mmm) cc_final: 0.8078 (mmp) REVERT: B 59 PHE cc_start: 0.8570 (p90) cc_final: 0.8212 (p90) REVERT: B 288 ASP cc_start: 0.8685 (t70) cc_final: 0.8355 (t0) REVERT: C 187 ASN cc_start: 0.9493 (m-40) cc_final: 0.8959 (m-40) REVERT: C 195 ILE cc_start: 0.9555 (tp) cc_final: 0.9305 (pt) REVERT: D 59 MET cc_start: 0.7271 (ppp) cc_final: 0.6997 (ppp) REVERT: D 150 ARG cc_start: 0.9144 (tmm-80) cc_final: 0.8699 (tmm-80) REVERT: D 162 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.9166 (t80) REVERT: D 177 TYR cc_start: 0.9008 (m-80) cc_final: 0.8615 (m-80) REVERT: E 61 MET cc_start: 0.7297 (tmm) cc_final: 0.6794 (tmm) REVERT: E 65 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9029 (mtmm) REVERT: E 130 CYS cc_start: 0.9536 (m) cc_final: 0.9323 (p) REVERT: E 150 ARG cc_start: 0.8664 (tmm-80) cc_final: 0.8039 (tmm-80) REVERT: E 184 LEU cc_start: 0.9547 (mt) cc_final: 0.9206 (mt) REVERT: F 95 GLU cc_start: 0.9135 (tp30) cc_final: 0.8696 (tm-30) REVERT: F 108 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8098 (tptt) REVERT: F 286 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8880 (t0) REVERT: F 354 MET cc_start: 0.6185 (tpt) cc_final: 0.5530 (tpt) REVERT: F 616 TYR cc_start: 0.8066 (m-80) cc_final: 0.7837 (m-80) REVERT: F 728 GLU cc_start: 0.9150 (mp0) cc_final: 0.8856 (mt-10) REVERT: F 778 PHE cc_start: 0.9288 (m-80) cc_final: 0.8659 (m-80) REVERT: F 841 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8946 (mttt) REVERT: F 910 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8355 (mt) REVERT: a 199 PHE cc_start: 0.8575 (t80) cc_final: 0.8206 (t80) REVERT: a 446 MET cc_start: 0.8859 (mmm) cc_final: 0.8617 (mmt) REVERT: b 13 CYS cc_start: 0.8975 (t) cc_final: 0.8711 (m) REVERT: b 14 MET cc_start: 0.8708 (ttt) cc_final: 0.8264 (tpp) REVERT: b 127 PHE cc_start: 0.7989 (m-10) cc_final: 0.7721 (m-10) REVERT: b 215 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7265 (mm) REVERT: b 306 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7811 (tp) REVERT: c 42 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: c 215 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8510 (mm110) REVERT: d 21 GLN cc_start: 0.8995 (tt0) cc_final: 0.8609 (tm-30) REVERT: d 61 MET cc_start: 0.7127 (ttp) cc_final: 0.6260 (tmm) REVERT: d 96 PHE cc_start: 0.8980 (p90) cc_final: 0.8649 (p90) REVERT: d 138 GLN cc_start: 0.9455 (tp40) cc_final: 0.9150 (tp40) REVERT: d 172 LEU cc_start: 0.9726 (OUTLIER) cc_final: 0.9491 (pp) REVERT: e 5 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8936 (mm) REVERT: e 125 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8819 (tm-30) REVERT: e 153 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8977 (tmm160) REVERT: f 761 TYR cc_start: 0.9378 (m-10) cc_final: 0.9065 (m-80) REVERT: f 774 LEU cc_start: 0.9834 (OUTLIER) cc_final: 0.9584 (tt) REVERT: f 812 MET cc_start: 0.8662 (ppp) cc_final: 0.8213 (ppp) outliers start: 139 outliers final: 77 residues processed: 518 average time/residue: 0.2280 time to fit residues: 193.3929 Evaluate side-chains 452 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 362 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 157 VAL 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 A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 65 LYS Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 841 LYS Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain F residue 910 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 409 TYR Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain b residue 415 ASN Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 215 GLN Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain e residue 145 GLN Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 770 ASP Chi-restraints excluded: chain f residue 774 LEU Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 805 TRP Chi-restraints excluded: chain f residue 825 VAL Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 346 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 345 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 410 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS D 145 GLN F 904 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.093908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060329 restraints weight = 206742.549| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.73 r_work: 0.2741 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 40216 Z= 0.212 Angle : 0.604 13.597 54875 Z= 0.320 Chirality : 0.042 0.281 6096 Planarity : 0.004 0.060 6532 Dihedral : 16.533 131.087 6468 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.70 % Allowed : 24.11 % Favored : 72.20 % 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 are not related in a simple way. whole: 1.29 (0.13), residues: 4454 helix: 2.28 (0.12), residues: 1746 sheet: 0.67 (0.19), residues: 725 loop : -0.36 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 109 TYR 0.024 0.001 TYR d 129 PHE 0.037 0.002 PHE f 664 TRP 0.033 0.001 TRP f 805 HIS 0.010 0.001 HIS C 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (40215) covalent geometry : angle 0.60438 / 0.32 (54875) hydrogen bonds : bond 0.04563 / 3.02 ( 1968) hydrogen bonds : angle 4.48935 / 3.15 ( 5539) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 377 time to evaluate : 1.503 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 336 GLU cc_start: 0.8858 (tp30) cc_final: 0.8597 (tp30) REVERT: A 421 ASP cc_start: 0.8246 (t0) cc_final: 0.7955 (t0) REVERT: A 453 MET cc_start: 0.8857 (mmm) cc_final: 0.8550 (mmm) REVERT: B 14 MET cc_start: 0.8416 (mmm) cc_final: 0.8121 (mmp) REVERT: B 59 PHE cc_start: 0.8563 (p90) cc_final: 0.8157 (p90) REVERT: B 288 ASP cc_start: 0.8727 (t70) cc_final: 0.8381 (t0) REVERT: B 452 ASN cc_start: 0.8891 (m-40) cc_final: 0.8619 (m-40) REVERT: C 109 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8090 (ttm110) REVERT: C 187 ASN cc_start: 0.9510 (m-40) cc_final: 0.8988 (m-40) REVERT: C 195 ILE cc_start: 0.9558 (tp) cc_final: 0.9247 (pt) REVERT: D 59 MET cc_start: 0.7472 (ppp) cc_final: 0.7214 (ppp) REVERT: D 61 MET cc_start: 0.7690 (tmm) cc_final: 0.7021 (tmm) REVERT: D 150 ARG cc_start: 0.9261 (tmm-80) cc_final: 0.8854 (tmm-80) REVERT: D 177 TYR cc_start: 0.9055 (m-80) cc_final: 0.8669 (m-80) REVERT: E 150 ARG cc_start: 0.8795 (tmm-80) cc_final: 0.8108 (tmm-80) REVERT: E 157 ASP cc_start: 0.9521 (m-30) cc_final: 0.9036 (t0) REVERT: F 95 GLU cc_start: 0.9228 (tp30) cc_final: 0.8784 (tm-30) REVERT: F 108 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8047 (tptt) REVERT: F 286 ASP cc_start: 0.9268 (OUTLIER) cc_final: 0.8923 (t0) REVERT: F 308 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: F 354 MET cc_start: 0.6129 (tpt) cc_final: 0.5467 (tpt) REVERT: F 616 TYR cc_start: 0.8148 (m-80) cc_final: 0.7871 (m-80) REVERT: F 728 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.8879 (mt-10) REVERT: F 778 PHE cc_start: 0.9358 (m-80) cc_final: 0.8656 (m-80) REVERT: F 910 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8486 (mt) REVERT: G 191 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8854 (mttp) REVERT: a 199 PHE cc_start: 0.8589 (t80) cc_final: 0.8221 (t80) REVERT: a 358 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.9084 (ttpt) REVERT: b 13 CYS cc_start: 0.8946 (t) cc_final: 0.8723 (m) REVERT: b 14 MET cc_start: 0.8700 (ttt) cc_final: 0.8285 (tpp) REVERT: b 127 PHE cc_start: 0.8071 (m-10) cc_final: 0.7677 (m-80) REVERT: b 292 GLU cc_start: 0.8968 (tt0) cc_final: 0.8490 (tp30) REVERT: b 306 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7786 (tp) REVERT: c 42 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: c 50 ASP cc_start: 0.7737 (p0) cc_final: 0.7518 (p0) REVERT: c 176 ARG cc_start: 0.7010 (ptt180) cc_final: 0.6714 (ptt180) REVERT: d 21 GLN cc_start: 0.9084 (tt0) cc_final: 0.8659 (tm-30) REVERT: d 61 MET cc_start: 0.7413 (ttp) cc_final: 0.6500 (tmm) REVERT: d 96 PHE cc_start: 0.9078 (p90) cc_final: 0.8820 (p90) REVERT: d 172 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9516 (pp) REVERT: e 5 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8896 (mm) REVERT: e 125 GLU cc_start: 0.9316 (OUTLIER) cc_final: 0.8896 (tm-30) REVERT: e 153 ARG cc_start: 0.9262 (ttp80) cc_final: 0.8999 (tmm160) REVERT: e 181 ILE cc_start: 0.9716 (OUTLIER) cc_final: 0.9450 (tp) REVERT: f 698 TYR cc_start: 0.8968 (t80) cc_final: 0.8618 (t80) REVERT: f 761 TYR cc_start: 0.9398 (m-10) cc_final: 0.9108 (m-80) REVERT: f 774 LEU cc_start: 0.9846 (OUTLIER) cc_final: 0.9579 (mt) REVERT: f 812 MET cc_start: 0.8724 (ppp) cc_final: 0.7957 (ppp) outliers start: 149 outliers final: 88 residues processed: 498 average time/residue: 0.2322 time to fit residues: 191.3819 Evaluate side-chains 446 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 345 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 97 CYS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain F residue 910 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain G residue 191 LYS Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 312 LEU Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain e residue 181 ILE Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 774 LEU Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 805 TRP Chi-restraints excluded: chain f residue 825 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 185 optimal weight: 2.9990 chunk 421 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 440 optimal weight: 7.9990 chunk 427 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 369 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 HIS C 89 HIS D 145 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.093988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.060369 restraints weight = 163420.371| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.03 r_work: 0.2774 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 40216 Z= 0.172 Angle : 0.593 15.092 54875 Z= 0.313 Chirality : 0.042 0.342 6096 Planarity : 0.004 0.053 6532 Dihedral : 16.579 130.480 6463 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.55 % Allowed : 24.31 % Favored : 72.15 % 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 are not related in a simple way. whole: 1.28 (0.13), residues: 4454 helix: 2.27 (0.12), residues: 1744 sheet: 0.71 (0.19), residues: 723 loop : -0.37 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 161 TYR 0.030 0.001 TYR d 129 PHE 0.044 0.001 PHE D 162 TRP 0.033 0.001 TRP f 805 HIS 0.020 0.001 HIS d 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (40215) covalent geometry : angle 0.59294 / 0.31 (54875) hydrogen bonds : bond 0.04405 / 2.92 ( 1968) hydrogen bonds : angle 4.42866 / 3.10 ( 5539) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 372 time to evaluate : 1.509 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: A 336 GLU cc_start: 0.8847 (tp30) cc_final: 0.8598 (tp30) REVERT: A 421 ASP cc_start: 0.8232 (t0) cc_final: 0.7955 (t0) REVERT: A 453 MET cc_start: 0.8846 (mmm) cc_final: 0.8538 (mmm) REVERT: B 14 MET cc_start: 0.8396 (mmm) cc_final: 0.8139 (mmp) REVERT: B 154 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 210 MET cc_start: 0.9516 (tmm) cc_final: 0.9024 (ptp) REVERT: B 288 ASP cc_start: 0.8692 (t70) cc_final: 0.8351 (t0) REVERT: B 452 ASN cc_start: 0.8867 (m-40) cc_final: 0.8591 (m-40) REVERT: C 65 LEU cc_start: 0.9350 (tp) cc_final: 0.9148 (tp) REVERT: C 109 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7917 (ttm110) REVERT: C 187 ASN cc_start: 0.9485 (m-40) cc_final: 0.8960 (m-40) REVERT: C 195 ILE cc_start: 0.9567 (tp) cc_final: 0.9249 (pt) REVERT: D 59 MET cc_start: 0.7228 (ppp) cc_final: 0.6893 (ppp) REVERT: D 150 ARG cc_start: 0.9269 (tmm-80) cc_final: 0.8906 (tmm-80) REVERT: D 177 TYR cc_start: 0.9083 (m-80) cc_final: 0.8642 (m-80) REVERT: E 150 ARG cc_start: 0.8838 (tmm-80) cc_final: 0.8093 (tmm-80) REVERT: E 157 ASP cc_start: 0.9448 (m-30) cc_final: 0.8979 (t0) REVERT: F 95 GLU cc_start: 0.9212 (tp30) cc_final: 0.8797 (tm-30) REVERT: F 108 LYS cc_start: 0.8678 (ttpt) cc_final: 0.8085 (tptt) REVERT: F 121 ASP cc_start: 0.8513 (m-30) cc_final: 0.8237 (m-30) REVERT: F 286 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8876 (t0) REVERT: F 308 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: F 354 MET cc_start: 0.6179 (tpt) cc_final: 0.5502 (tpt) REVERT: F 616 TYR cc_start: 0.8083 (m-80) cc_final: 0.7832 (m-80) REVERT: F 671 ASP cc_start: 0.9233 (OUTLIER) cc_final: 0.9019 (t0) REVERT: F 728 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8844 (mt-10) REVERT: F 910 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8502 (mt) REVERT: G 191 LYS cc_start: 0.9261 (mttp) cc_final: 0.9021 (mttp) REVERT: a 134 MET cc_start: 0.9125 (tmm) cc_final: 0.8797 (tmm) REVERT: a 135 MET cc_start: 0.8859 (mmm) cc_final: 0.8361 (mmm) REVERT: a 199 PHE cc_start: 0.8596 (t80) cc_final: 0.8256 (t80) REVERT: a 358 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9129 (ttpt) REVERT: a 371 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: b 13 CYS cc_start: 0.8928 (t) cc_final: 0.8701 (m) REVERT: b 14 MET cc_start: 0.8704 (ttt) cc_final: 0.8263 (tpp) REVERT: b 127 PHE cc_start: 0.8075 (m-10) cc_final: 0.7673 (m-80) REVERT: b 215 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7246 (mm) REVERT: b 292 GLU cc_start: 0.8959 (tt0) cc_final: 0.8483 (tp30) REVERT: b 306 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7822 (tp) REVERT: c 42 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (mp10) REVERT: c 50 ASP cc_start: 0.7680 (p0) cc_final: 0.7466 (p0) REVERT: c 176 ARG cc_start: 0.7014 (ptt180) cc_final: 0.6771 (ptt180) REVERT: d 21 GLN cc_start: 0.9038 (tt0) cc_final: 0.8615 (tm-30) REVERT: d 58 ASP cc_start: 0.9753 (m-30) cc_final: 0.9398 (p0) REVERT: d 59 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8767 (ttp) REVERT: d 61 MET cc_start: 0.7299 (ttp) cc_final: 0.6425 (tmm) REVERT: d 96 PHE cc_start: 0.9061 (p90) cc_final: 0.8768 (p90) REVERT: d 172 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9503 (pp) REVERT: e 59 MET cc_start: 0.9074 (tpp) cc_final: 0.8073 (mmm) REVERT: e 125 GLU cc_start: 0.9276 (OUTLIER) cc_final: 0.8840 (tm-30) REVERT: e 153 ARG cc_start: 0.9254 (ttp80) cc_final: 0.8994 (tmm160) REVERT: f 698 TYR cc_start: 0.8952 (t80) cc_final: 0.8603 (t80) REVERT: f 761 TYR cc_start: 0.9346 (m-10) cc_final: 0.9052 (m-80) REVERT: f 774 LEU cc_start: 0.9843 (OUTLIER) cc_final: 0.9628 (tt) REVERT: f 812 MET cc_start: 0.8801 (ppp) cc_final: 0.7994 (ppp) outliers start: 143 outliers final: 89 residues processed: 485 average time/residue: 0.2375 time to fit residues: 190.5968 Evaluate side-chains 456 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 352 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 112 ASN Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 458 LEU Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 671 ASP Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain F residue 910 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 371 GLU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain c residue 216 ASP Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 166 VAL Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain f residue 659 PHE Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 774 LEU Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 256 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 313 optimal weight: 0.7980 chunk 222 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 120 optimal weight: 0.0670 chunk 426 optimal weight: 0.9990 chunk 397 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 390 optimal weight: 0.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN D 145 GLN c 215 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.094719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.061009 restraints weight = 176933.525| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.22 r_work: 0.2789 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40216 Z= 0.125 Angle : 0.578 14.428 54875 Z= 0.305 Chirality : 0.041 0.254 6096 Planarity : 0.004 0.053 6532 Dihedral : 16.540 129.210 6463 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.95 % Allowed : 24.75 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.13), residues: 4454 helix: 2.30 (0.13), residues: 1742 sheet: 0.80 (0.19), residues: 739 loop : -0.34 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 185 TYR 0.028 0.001 TYR d 129 PHE 0.029 0.001 PHE B 107 TRP 0.030 0.001 TRP f 805 HIS 0.005 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (40215) covalent geometry : angle 0.57845 / 0.30 (54875) hydrogen bonds : bond 0.04152 / 2.75 ( 1968) hydrogen bonds : angle 4.30662 / 3.02 ( 5539) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 380 time to evaluate : 1.595 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: A 336 GLU cc_start: 0.8842 (tp30) cc_final: 0.8569 (tp30) REVERT: A 421 ASP cc_start: 0.8225 (t0) cc_final: 0.7924 (t0) REVERT: A 453 MET cc_start: 0.8873 (mmm) cc_final: 0.8530 (mmm) REVERT: B 288 ASP cc_start: 0.8684 (t70) cc_final: 0.8329 (t0) REVERT: B 452 ASN cc_start: 0.8879 (m-40) cc_final: 0.8603 (m-40) REVERT: C 187 ASN cc_start: 0.9479 (m-40) cc_final: 0.8946 (m-40) REVERT: D 59 MET cc_start: 0.7401 (ppp) cc_final: 0.6992 (ppp) REVERT: D 130 CYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8904 (t) REVERT: D 150 ARG cc_start: 0.9274 (tmm-80) cc_final: 0.8894 (tmm-80) REVERT: D 177 TYR cc_start: 0.9067 (m-80) cc_final: 0.8629 (m-80) REVERT: E 150 ARG cc_start: 0.8880 (tmm-80) cc_final: 0.8165 (tmm-80) REVERT: E 157 ASP cc_start: 0.9438 (m-30) cc_final: 0.8852 (t0) REVERT: F 95 GLU cc_start: 0.9204 (tp30) cc_final: 0.8800 (tm-30) REVERT: F 108 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8060 (tptt) REVERT: F 121 ASP cc_start: 0.8544 (m-30) cc_final: 0.8251 (m-30) REVERT: F 286 ASP cc_start: 0.9242 (OUTLIER) cc_final: 0.8900 (t0) REVERT: F 308 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: F 354 MET cc_start: 0.6215 (tpt) cc_final: 0.5487 (tpt) REVERT: F 616 TYR cc_start: 0.8097 (m-80) cc_final: 0.7856 (m-80) REVERT: F 671 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.9032 (t0) REVERT: F 725 TRP cc_start: 0.8900 (t60) cc_final: 0.8477 (t60) REVERT: F 728 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8837 (mt-10) REVERT: F 746 MET cc_start: 0.8654 (mtp) cc_final: 0.8388 (mtp) REVERT: F 778 PHE cc_start: 0.9349 (m-80) cc_final: 0.8544 (m-80) REVERT: F 812 MET cc_start: 0.8043 (ppp) cc_final: 0.7281 (ppp) REVERT: a 199 PHE cc_start: 0.8607 (t80) cc_final: 0.8298 (t80) REVERT: a 533 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8909 (p0) REVERT: b 14 MET cc_start: 0.8728 (ttt) cc_final: 0.8271 (tpp) REVERT: b 127 PHE cc_start: 0.8089 (m-10) cc_final: 0.7681 (m-80) REVERT: b 215 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7111 (mm) REVERT: b 292 GLU cc_start: 0.8986 (tt0) cc_final: 0.8557 (tp30) REVERT: b 306 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7844 (tp) REVERT: c 42 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: c 50 ASP cc_start: 0.7694 (p0) cc_final: 0.7476 (p0) REVERT: c 176 ARG cc_start: 0.7028 (ptt180) cc_final: 0.6801 (ptt180) REVERT: d 21 GLN cc_start: 0.9038 (tt0) cc_final: 0.8529 (tm-30) REVERT: d 58 ASP cc_start: 0.9742 (m-30) cc_final: 0.9497 (p0) REVERT: d 96 PHE cc_start: 0.9044 (p90) cc_final: 0.8670 (p90) REVERT: d 172 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9524 (pp) REVERT: e 5 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8909 (mm) REVERT: e 59 MET cc_start: 0.9017 (tpp) cc_final: 0.8244 (mmm) REVERT: e 153 ARG cc_start: 0.9255 (ttp80) cc_final: 0.8994 (tmm160) REVERT: f 698 TYR cc_start: 0.8914 (t80) cc_final: 0.8548 (t80) REVERT: f 735 PHE cc_start: 0.8273 (t80) cc_final: 0.7794 (t80) REVERT: f 743 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7253 (tmm) REVERT: f 761 TYR cc_start: 0.9305 (m-10) cc_final: 0.9012 (m-80) REVERT: f 812 MET cc_start: 0.8816 (ppp) cc_final: 0.7981 (ppp) outliers start: 119 outliers final: 77 residues processed: 473 average time/residue: 0.2445 time to fit residues: 189.5870 Evaluate side-chains 446 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 357 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 281 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 A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 671 ASP Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 245 ILE Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 110 optimal weight: 2.9990 chunk 387 optimal weight: 0.9980 chunk 437 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 337 optimal weight: 4.9990 chunk 444 optimal weight: 4.9990 chunk 428 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 95 ASN A 101 ASN D 145 GLN ** d 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.060606 restraints weight = 178093.954| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 4.14 r_work: 0.2780 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40216 Z= 0.151 Angle : 0.587 14.285 54875 Z= 0.307 Chirality : 0.041 0.392 6096 Planarity : 0.004 0.053 6532 Dihedral : 16.557 129.614 6458 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.03 % Allowed : 24.53 % Favored : 72.45 % 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 are not related in a simple way. whole: 1.35 (0.13), residues: 4454 helix: 2.28 (0.13), residues: 1747 sheet: 0.83 (0.19), residues: 739 loop : -0.34 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 71 TYR 0.028 0.001 TYR d 129 PHE 0.029 0.001 PHE B 107 TRP 0.029 0.001 TRP f 805 HIS 0.025 0.001 HIS d 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (40215) covalent geometry : angle 0.58691 / 0.31 (54875) hydrogen bonds : bond 0.04171 / 2.76 ( 1968) hydrogen bonds : angle 4.30270 / 3.02 ( 5539) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 374 time to evaluate : 1.828 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: A 218 ARG cc_start: 0.8935 (ttm-80) cc_final: 0.8689 (ttp80) REVERT: A 336 GLU cc_start: 0.8856 (tp30) cc_final: 0.8610 (tp30) REVERT: A 421 ASP cc_start: 0.8206 (t0) cc_final: 0.7910 (t0) REVERT: A 453 MET cc_start: 0.8871 (mmm) cc_final: 0.8548 (mmm) REVERT: B 14 MET cc_start: 0.8258 (mmm) cc_final: 0.7958 (mmp) REVERT: B 288 ASP cc_start: 0.8686 (t70) cc_final: 0.8316 (t0) REVERT: B 452 ASN cc_start: 0.8886 (m-40) cc_final: 0.8590 (m-40) REVERT: C 187 ASN cc_start: 0.9478 (m-40) cc_final: 0.9166 (m-40) REVERT: C 195 ILE cc_start: 0.9519 (tp) cc_final: 0.9287 (pt) REVERT: D 59 MET cc_start: 0.7501 (ppp) cc_final: 0.7066 (ppp) REVERT: D 130 CYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8907 (t) REVERT: D 150 ARG cc_start: 0.9298 (tmm-80) cc_final: 0.8938 (tmm-80) REVERT: D 176 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9179 (pp) REVERT: D 177 TYR cc_start: 0.9111 (m-80) cc_final: 0.8425 (m-80) REVERT: E 150 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8321 (tmm-80) REVERT: E 157 ASP cc_start: 0.9427 (m-30) cc_final: 0.8815 (t0) REVERT: F 95 GLU cc_start: 0.9207 (tp30) cc_final: 0.8810 (tm-30) REVERT: F 108 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8086 (tptt) REVERT: F 121 ASP cc_start: 0.8565 (m-30) cc_final: 0.8274 (m-30) REVERT: F 308 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8473 (pm20) REVERT: F 354 MET cc_start: 0.6172 (tpt) cc_final: 0.5418 (tpt) REVERT: F 616 TYR cc_start: 0.8149 (m-80) cc_final: 0.7907 (m-80) REVERT: F 725 TRP cc_start: 0.8896 (t60) cc_final: 0.8515 (t60) REVERT: F 728 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8830 (mt-10) REVERT: F 778 PHE cc_start: 0.9349 (m-80) cc_final: 0.8695 (m-80) REVERT: a 134 MET cc_start: 0.9282 (tmm) cc_final: 0.8862 (tmm) REVERT: a 199 PHE cc_start: 0.8643 (t80) cc_final: 0.8353 (t80) REVERT: a 358 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.9101 (ttpt) REVERT: a 371 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: a 533 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8905 (p0) REVERT: b 14 MET cc_start: 0.8693 (ttt) cc_final: 0.8013 (tpp) REVERT: b 20 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.6420 (ptm) REVERT: b 127 PHE cc_start: 0.8129 (m-10) cc_final: 0.7706 (m-80) REVERT: b 215 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7169 (mm) REVERT: b 277 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8262 (p) REVERT: b 292 GLU cc_start: 0.8948 (tt0) cc_final: 0.8498 (tp30) REVERT: b 306 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7852 (tp) REVERT: c 42 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: c 50 ASP cc_start: 0.7712 (p0) cc_final: 0.7492 (p0) REVERT: c 176 ARG cc_start: 0.7049 (ptt180) cc_final: 0.6799 (ptt180) REVERT: d 21 GLN cc_start: 0.8876 (tt0) cc_final: 0.8544 (tm-30) REVERT: d 59 MET cc_start: 0.8628 (ttp) cc_final: 0.8399 (ptm) REVERT: d 66 TYR cc_start: 0.9458 (t80) cc_final: 0.9066 (t80) REVERT: d 96 PHE cc_start: 0.9035 (p90) cc_final: 0.8672 (p90) REVERT: d 172 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9523 (pp) REVERT: e 153 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8989 (tmm160) REVERT: f 698 TYR cc_start: 0.8935 (t80) cc_final: 0.8589 (t80) REVERT: f 735 PHE cc_start: 0.8291 (t80) cc_final: 0.7830 (t80) REVERT: f 761 TYR cc_start: 0.9278 (m-10) cc_final: 0.9039 (m-80) REVERT: f 812 MET cc_start: 0.8817 (ppp) cc_final: 0.7963 (ppp) outliers start: 122 outliers final: 86 residues processed: 471 average time/residue: 0.2432 time to fit residues: 188.3468 Evaluate side-chains 451 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 352 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 371 GLU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 13 CYS Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain d residue 184 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain f residue 659 PHE Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 353 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 354 optimal weight: 0.6980 chunk 260 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 442 optimal weight: 7.9990 chunk 426 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 253 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 145 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.093806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.060644 restraints weight = 178535.654| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.09 r_work: 0.2793 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2790 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2790 r_free = 0.2790 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2790 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40216 Z= 0.153 Angle : 0.603 15.378 54875 Z= 0.313 Chirality : 0.041 0.335 6096 Planarity : 0.004 0.060 6532 Dihedral : 16.587 129.359 6458 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.83 % Allowed : 25.15 % Favored : 72.02 % 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 are not related in a simple way. whole: 1.32 (0.13), residues: 4454 helix: 2.24 (0.13), residues: 1753 sheet: 0.83 (0.19), residues: 733 loop : -0.35 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 161 TYR 0.029 0.001 TYR d 129 PHE 0.029 0.001 PHE B 107 TRP 0.029 0.001 TRP f 805 HIS 0.008 0.001 HIS d 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (40215) covalent geometry : angle 0.60256 / 0.31 (54875) hydrogen bonds : bond 0.04144 / 2.73 ( 1968) hydrogen bonds : angle 4.30785 / 3.02 ( 5539) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 360 time to evaluate : 1.888 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: A 218 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8684 (ttp80) REVERT: A 336 GLU cc_start: 0.8832 (tp30) cc_final: 0.8585 (tp30) REVERT: A 421 ASP cc_start: 0.8186 (t0) cc_final: 0.7893 (t0) REVERT: A 453 MET cc_start: 0.8855 (mmm) cc_final: 0.8543 (mmm) REVERT: B 14 MET cc_start: 0.8279 (mmm) cc_final: 0.8017 (mmp) REVERT: B 452 ASN cc_start: 0.8884 (m-40) cc_final: 0.8595 (m-40) REVERT: C 195 ILE cc_start: 0.9527 (tp) cc_final: 0.9291 (pt) REVERT: D 59 MET cc_start: 0.7481 (ppp) cc_final: 0.7007 (ppp) REVERT: D 130 CYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8879 (t) REVERT: D 150 ARG cc_start: 0.9320 (tmm-80) cc_final: 0.8829 (tmm-80) REVERT: D 176 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9185 (pp) REVERT: D 177 TYR cc_start: 0.9055 (m-80) cc_final: 0.8367 (m-80) REVERT: E 150 ARG cc_start: 0.8910 (tmm-80) cc_final: 0.8320 (tmm-80) REVERT: F 95 GLU cc_start: 0.9182 (tp30) cc_final: 0.8809 (tm-30) REVERT: F 108 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8135 (tptt) REVERT: F 121 ASP cc_start: 0.8576 (m-30) cc_final: 0.8293 (m-30) REVERT: F 286 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8857 (t0) REVERT: F 308 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: F 354 MET cc_start: 0.6152 (tpt) cc_final: 0.5427 (tpt) REVERT: F 616 TYR cc_start: 0.8105 (m-80) cc_final: 0.7874 (m-80) REVERT: F 725 TRP cc_start: 0.8855 (t60) cc_final: 0.8515 (t60) REVERT: F 728 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: F 778 PHE cc_start: 0.9200 (m-80) cc_final: 0.8556 (m-80) REVERT: a 134 MET cc_start: 0.9250 (tmm) cc_final: 0.8838 (tmm) REVERT: a 199 PHE cc_start: 0.8683 (t80) cc_final: 0.8416 (t80) REVERT: a 358 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9123 (ttpt) REVERT: a 371 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: a 533 ASP cc_start: 0.9110 (OUTLIER) cc_final: 0.8900 (p0) REVERT: b 14 MET cc_start: 0.8700 (ttt) cc_final: 0.8325 (tpp) REVERT: b 20 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6187 (ptm) REVERT: b 127 PHE cc_start: 0.8140 (m-10) cc_final: 0.7728 (m-80) REVERT: b 210 MET cc_start: 0.9261 (ppp) cc_final: 0.8944 (pmm) REVERT: b 215 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7238 (mm) REVERT: b 277 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8276 (p) REVERT: b 292 GLU cc_start: 0.8929 (tt0) cc_final: 0.8485 (tp30) REVERT: b 306 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.7961 (tp) REVERT: c 42 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: c 50 ASP cc_start: 0.7718 (p0) cc_final: 0.7494 (p0) REVERT: d 21 GLN cc_start: 0.8818 (tt0) cc_final: 0.8535 (tm-30) REVERT: d 59 MET cc_start: 0.8757 (ttp) cc_final: 0.8355 (ptm) REVERT: d 66 TYR cc_start: 0.9513 (t80) cc_final: 0.9018 (t80) REVERT: d 96 PHE cc_start: 0.8974 (p90) cc_final: 0.8596 (p90) REVERT: d 172 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9531 (pp) REVERT: e 59 MET cc_start: 0.8995 (mmm) cc_final: 0.8564 (mmm) REVERT: e 153 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8955 (tmm160) REVERT: f 698 TYR cc_start: 0.8878 (t80) cc_final: 0.8569 (t80) REVERT: f 735 PHE cc_start: 0.8305 (t80) cc_final: 0.7870 (t80) REVERT: f 761 TYR cc_start: 0.9177 (m-10) cc_final: 0.8908 (m-80) REVERT: f 812 MET cc_start: 0.8777 (ppp) cc_final: 0.7872 (ppp) outliers start: 114 outliers final: 86 residues processed: 452 average time/residue: 0.2338 time to fit residues: 173.9097 Evaluate side-chains 449 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 349 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 781 ILE Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 371 GLU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 13 CYS Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 89 SER Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 30 optimal weight: 0.7980 chunk 256 optimal weight: 10.0000 chunk 416 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 294 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 228 optimal weight: 5.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 145 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.093735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.060663 restraints weight = 166171.447| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.98 r_work: 0.2796 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40216 Z= 0.155 Angle : 0.607 13.890 54875 Z= 0.316 Chirality : 0.041 0.315 6096 Planarity : 0.004 0.051 6532 Dihedral : 16.602 129.222 6458 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.90 % Allowed : 25.02 % Favored : 72.07 % 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 are not related in a simple way. whole: 1.32 (0.13), residues: 4454 helix: 2.21 (0.13), residues: 1748 sheet: 0.82 (0.19), residues: 720 loop : -0.30 (0.14), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG d 161 TYR 0.026 0.001 TYR d 129 PHE 0.029 0.001 PHE B 107 TRP 0.028 0.001 TRP f 805 HIS 0.004 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (40215) covalent geometry : angle 0.60733 / 0.32 (54875) hydrogen bonds : bond 0.04135 / 2.73 ( 1968) hydrogen bonds : angle 4.30482 / 3.02 ( 5539) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 359 time to evaluate : 1.700 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: A 218 ARG cc_start: 0.8910 (ttm-80) cc_final: 0.8677 (ttp80) REVERT: A 336 GLU cc_start: 0.8837 (tp30) cc_final: 0.8589 (tp30) REVERT: A 421 ASP cc_start: 0.8170 (t0) cc_final: 0.7880 (t0) REVERT: A 453 MET cc_start: 0.8871 (mmm) cc_final: 0.8558 (mmm) REVERT: B 14 MET cc_start: 0.8313 (mmm) cc_final: 0.8081 (mmp) REVERT: B 154 LEU cc_start: 0.8507 (mm) cc_final: 0.8300 (mt) REVERT: B 452 ASN cc_start: 0.8882 (m-40) cc_final: 0.8590 (m-40) REVERT: C 195 ILE cc_start: 0.9530 (tp) cc_final: 0.9283 (pt) REVERT: D 59 MET cc_start: 0.7552 (ppp) cc_final: 0.7037 (ppp) REVERT: D 130 CYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8882 (t) REVERT: D 150 ARG cc_start: 0.9353 (tmm-80) cc_final: 0.8965 (tmm-80) REVERT: D 176 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9196 (pp) REVERT: D 177 TYR cc_start: 0.9068 (m-80) cc_final: 0.8365 (m-80) REVERT: E 150 ARG cc_start: 0.8924 (tmm-80) cc_final: 0.8320 (tmm-80) REVERT: F 95 GLU cc_start: 0.9167 (tp30) cc_final: 0.8799 (tm-30) REVERT: F 108 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8137 (tptt) REVERT: F 121 ASP cc_start: 0.8559 (m-30) cc_final: 0.8275 (m-30) REVERT: F 286 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8847 (t0) REVERT: F 308 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: F 354 MET cc_start: 0.6167 (tpt) cc_final: 0.5407 (tpt) REVERT: F 616 TYR cc_start: 0.8102 (m-80) cc_final: 0.7872 (m-80) REVERT: F 725 TRP cc_start: 0.8851 (t60) cc_final: 0.8515 (t60) REVERT: F 728 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: F 746 MET cc_start: 0.8932 (mmm) cc_final: 0.8450 (mmt) REVERT: F 778 PHE cc_start: 0.9193 (m-80) cc_final: 0.8527 (m-80) REVERT: a 134 MET cc_start: 0.9236 (tmm) cc_final: 0.8827 (tmm) REVERT: a 199 PHE cc_start: 0.8672 (t80) cc_final: 0.8410 (t80) REVERT: a 358 LYS cc_start: 0.9411 (OUTLIER) cc_final: 0.9132 (ttpt) REVERT: a 371 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: a 533 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8885 (p0) REVERT: b 14 MET cc_start: 0.8660 (ttt) cc_final: 0.8274 (tpp) REVERT: b 20 MET cc_start: 0.6684 (OUTLIER) cc_final: 0.6181 (ptm) REVERT: b 127 PHE cc_start: 0.8171 (m-10) cc_final: 0.7759 (m-80) REVERT: b 215 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7238 (mm) REVERT: b 277 THR cc_start: 0.8805 (OUTLIER) cc_final: 0.8270 (p) REVERT: b 292 GLU cc_start: 0.8930 (tt0) cc_final: 0.8483 (tp30) REVERT: b 306 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7992 (tp) REVERT: c 42 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (mp10) REVERT: c 50 ASP cc_start: 0.7705 (p0) cc_final: 0.7484 (p0) REVERT: d 21 GLN cc_start: 0.8829 (tt0) cc_final: 0.8533 (tm-30) REVERT: d 59 MET cc_start: 0.8793 (ttp) cc_final: 0.8456 (ptm) REVERT: d 66 TYR cc_start: 0.9515 (t80) cc_final: 0.9011 (t80) REVERT: d 96 PHE cc_start: 0.9004 (p90) cc_final: 0.8591 (p90) REVERT: d 172 LEU cc_start: 0.9756 (OUTLIER) cc_final: 0.9537 (pp) REVERT: e 59 MET cc_start: 0.8988 (mmm) cc_final: 0.8577 (mmm) REVERT: e 125 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: e 153 ARG cc_start: 0.9216 (ttp80) cc_final: 0.8940 (tmm160) REVERT: f 698 TYR cc_start: 0.8865 (t80) cc_final: 0.8558 (t80) REVERT: f 735 PHE cc_start: 0.8291 (t80) cc_final: 0.7868 (t80) REVERT: f 761 TYR cc_start: 0.9135 (m-10) cc_final: 0.8869 (m-80) REVERT: f 812 MET cc_start: 0.8783 (ppp) cc_final: 0.7884 (ppp) outliers start: 117 outliers final: 89 residues processed: 450 average time/residue: 0.2395 time to fit residues: 179.1346 Evaluate side-chains 457 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 353 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 142 SER Chi-restraints excluded: chain a residue 168 LEU Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 371 GLU Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 13 CYS Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 277 THR Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain c residue 179 LEU Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 267 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 388 optimal weight: 0.8980 chunk 173 optimal weight: 0.6980 chunk 356 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 225 optimal weight: 0.4980 chunk 319 optimal weight: 0.0570 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 320 GLN D 145 GLN f 862 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.094122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061578 restraints weight = 144969.801| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.71 r_work: 0.2818 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 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 = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40216 Z= 0.123 Angle : 0.612 15.060 54875 Z= 0.316 Chirality : 0.042 0.444 6096 Planarity : 0.004 0.051 6532 Dihedral : 16.561 128.284 6458 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.68 % Allowed : 25.25 % Favored : 72.07 % 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 are not related in a simple way. whole: 1.34 (0.13), residues: 4454 helix: 2.23 (0.13), residues: 1745 sheet: 0.88 (0.19), residues: 728 loop : -0.30 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 161 TYR 0.025 0.001 TYR d 129 PHE 0.030 0.001 PHE B 107 TRP 0.029 0.001 TRP f 805 HIS 0.004 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (40215) covalent geometry : angle 0.61156 / 0.32 (54875) hydrogen bonds : bond 0.03999 / 2.65 ( 1968) hydrogen bonds : angle 4.27558 / 3.00 ( 5539) Misc. bond : bond 0.00016 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8908 Ramachandran restraints generated. 4454 Oldfield, 0 Emsley, 4454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 365 time to evaluate : 1.365 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: A 218 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8691 (ttp80) REVERT: A 336 GLU cc_start: 0.8828 (tp30) cc_final: 0.8557 (tp30) REVERT: A 421 ASP cc_start: 0.8174 (t0) cc_final: 0.7887 (t0) REVERT: A 453 MET cc_start: 0.8883 (mmm) cc_final: 0.8536 (mmm) REVERT: B 14 MET cc_start: 0.8325 (mmm) cc_final: 0.8089 (mmp) REVERT: B 154 LEU cc_start: 0.8528 (mm) cc_final: 0.8325 (mt) REVERT: B 212 MET cc_start: 0.8972 (tmm) cc_final: 0.8660 (tmm) REVERT: B 452 ASN cc_start: 0.8863 (m-40) cc_final: 0.8571 (m-40) REVERT: C 94 THR cc_start: 0.8705 (m) cc_final: 0.8268 (p) REVERT: C 195 ILE cc_start: 0.9525 (tp) cc_final: 0.9275 (pt) REVERT: D 59 MET cc_start: 0.7611 (ppp) cc_final: 0.7105 (ppp) REVERT: D 130 CYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8868 (t) REVERT: D 150 ARG cc_start: 0.9344 (tmm-80) cc_final: 0.9088 (tmm-80) REVERT: D 176 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9187 (pp) REVERT: D 177 TYR cc_start: 0.9078 (m-80) cc_final: 0.8385 (m-80) REVERT: E 150 ARG cc_start: 0.8946 (tmm-80) cc_final: 0.8323 (tmm-80) REVERT: F 95 GLU cc_start: 0.9156 (tp30) cc_final: 0.8811 (tm-30) REVERT: F 108 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8103 (tptt) REVERT: F 121 ASP cc_start: 0.8546 (m-30) cc_final: 0.8263 (m-30) REVERT: F 286 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8850 (t0) REVERT: F 308 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: F 354 MET cc_start: 0.6124 (tpt) cc_final: 0.5351 (tpt) REVERT: F 616 TYR cc_start: 0.8105 (m-80) cc_final: 0.7882 (m-80) REVERT: F 725 TRP cc_start: 0.8865 (t60) cc_final: 0.8540 (t60) REVERT: F 728 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8819 (mt-10) REVERT: F 778 PHE cc_start: 0.9220 (m-80) cc_final: 0.8403 (m-80) REVERT: G 191 LYS cc_start: 0.9039 (ptpp) cc_final: 0.8798 (ptpp) REVERT: a 134 MET cc_start: 0.9214 (tmm) cc_final: 0.8803 (tmm) REVERT: a 199 PHE cc_start: 0.8663 (t80) cc_final: 0.8419 (t80) REVERT: a 358 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.9122 (ttpt) REVERT: a 533 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8887 (p0) REVERT: b 14 MET cc_start: 0.8619 (ttt) cc_final: 0.8206 (tpp) REVERT: b 20 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6137 (ptm) REVERT: b 99 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8428 (mm-40) REVERT: b 127 PHE cc_start: 0.8139 (m-10) cc_final: 0.7699 (m-80) REVERT: b 215 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7296 (mm) REVERT: b 292 GLU cc_start: 0.8924 (tt0) cc_final: 0.8477 (tp30) REVERT: b 306 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7969 (tp) REVERT: c 42 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: c 50 ASP cc_start: 0.7611 (p0) cc_final: 0.7397 (p0) REVERT: d 21 GLN cc_start: 0.8890 (tt0) cc_final: 0.8529 (tm-30) REVERT: d 59 MET cc_start: 0.8809 (ttp) cc_final: 0.8436 (ptm) REVERT: d 66 TYR cc_start: 0.9513 (t80) cc_final: 0.9001 (t80) REVERT: d 96 PHE cc_start: 0.9007 (p90) cc_final: 0.8577 (p90) REVERT: d 172 LEU cc_start: 0.9767 (OUTLIER) cc_final: 0.9565 (pp) REVERT: d 192 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8587 (mmm160) REVERT: e 59 MET cc_start: 0.9000 (mmm) cc_final: 0.8568 (mmm) REVERT: e 153 ARG cc_start: 0.9229 (ttp80) cc_final: 0.8965 (tmm160) REVERT: f 698 TYR cc_start: 0.8889 (t80) cc_final: 0.8568 (t80) REVERT: f 735 PHE cc_start: 0.8291 (t80) cc_final: 0.7851 (t80) REVERT: f 761 TYR cc_start: 0.9136 (m-10) cc_final: 0.8861 (m-80) REVERT: f 812 MET cc_start: 0.8789 (ppp) cc_final: 0.7966 (ppp) outliers start: 108 outliers final: 83 residues processed: 452 average time/residue: 0.2250 time to fit residues: 168.8531 Evaluate side-chains 455 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 359 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain B residue 152 HIS Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 95 PHE Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 145 GLN Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 106 PHE Chi-restraints excluded: chain E residue 114 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain F residue 200 GLN Chi-restraints excluded: chain F residue 213 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 368 ASP Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 728 GLU Chi-restraints excluded: chain F residue 742 PHE Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 898 ILE Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 200 LEU Chi-restraints excluded: chain a residue 206 LYS Chi-restraints excluded: chain a residue 242 LEU Chi-restraints excluded: chain a residue 314 SER Chi-restraints excluded: chain a residue 358 LYS Chi-restraints excluded: chain a residue 435 VAL Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 522 VAL Chi-restraints excluded: chain a residue 529 VAL Chi-restraints excluded: chain a residue 533 ASP Chi-restraints excluded: chain b residue 11 VAL Chi-restraints excluded: chain b residue 20 MET Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain b residue 142 PHE Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 246 HIS Chi-restraints excluded: chain b residue 289 ILE Chi-restraints excluded: chain b residue 306 LEU Chi-restraints excluded: chain b residue 357 MET Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 97 CYS Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 ASP Chi-restraints excluded: chain d residue 9 HIS Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 89 SER Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 167 SER Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 104 VAL Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 667 MET Chi-restraints excluded: chain f residue 701 ILE Chi-restraints excluded: chain f residue 781 ILE Chi-restraints excluded: chain f residue 825 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 164 optimal weight: 7.9990 chunk 439 optimal weight: 0.7980 chunk 393 optimal weight: 4.9990 chunk 269 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 336 optimal weight: 6.9990 chunk 432 optimal weight: 0.6980 chunk 337 optimal weight: 0.9980 chunk 451 optimal weight: 40.0000 chunk 171 optimal weight: 0.6980 chunk 398 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 132 GLN A 320 GLN D 145 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.093668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.060645 restraints weight = 166844.275| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.99 r_work: 0.2803 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 40216 Z= 0.150 Angle : 0.621 14.368 54875 Z= 0.321 Chirality : 0.042 0.403 6096 Planarity : 0.004 0.051 6532 Dihedral : 16.582 128.627 6458 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.58 % Allowed : 25.47 % Favored : 71.95 % 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 are not related in a simple way. whole: 1.33 (0.13), residues: 4454 helix: 2.22 (0.13), residues: 1745 sheet: 0.85 (0.19), residues: 720 loop : -0.29 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 161 TYR 0.024 0.001 TYR d 129 PHE 0.029 0.001 PHE B 107 TRP 0.034 0.001 TRP F 893 HIS 0.004 0.001 HIS c 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (40215) covalent geometry : angle 0.62122 / 0.32 (54875) hydrogen bonds : bond 0.04068 / 2.70 ( 1968) hydrogen bonds : angle 4.29143 / 3.00 ( 5539) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16678.38 seconds wall clock time: 284 minutes 3.23 seconds (17043.23 seconds total)