Starting phenix.real_space_refine on Tue Aug 26 16:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n83_49110/08_2025/9n83_49110.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n83_49110/08_2025/9n83_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_49110/08_2025/9n83_49110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n83_49110/08_2025/9n83_49110.map" model { file = "/net/cci-nas-00/data/ceres_data/9n83_49110/08_2025/9n83_49110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n83_49110/08_2025/9n83_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 11.95, per 1000 atoms: 0.31 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: 4.56 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 6.00 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: 11.02 Time building geometry restraints manager: 5.67 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=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.17e+00 bond pdb=" N MET d 1 " pdb=" CA MET d 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 bond pdb=" N VAL c 0 " pdb=" CA VAL c 0 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 40210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 53888 1.66 - 3.32: 846 3.32 - 4.99: 126 4.99 - 6.65: 12 6.65 - 8.31: 3 Bond angle restraints: 54875 Sorted by residual: angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" C VAL A 427 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" C1' AMP L1001 " pdb=" C2' AMP L1001 " pdb=" C3' AMP L1001 " ideal model delta sigma weight residual 111.00 102.69 8.31 3.00e+00 1.11e-01 7.67e+00 angle pdb=" C3' DT J 67 " pdb=" C2' DT J 67 " pdb=" C1' DT J 67 " ideal model delta sigma weight residual 101.60 105.71 -4.11 1.50e+00 4.44e-01 7.49e+00 angle pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " pdb=" CD GLU B 128 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.70e+00 3.46e-01 7.08e+00 angle pdb=" C SER F 804 " pdb=" N TRP F 805 " pdb=" CA TRP F 805 " ideal model delta sigma weight residual 120.72 125.06 -4.34 1.67e+00 3.59e-01 6.76e+00 ... (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: 4829 0.044 - 0.087: 896 0.087 - 0.131: 356 0.131 - 0.175: 14 0.175 - 0.218: 1 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=" CG LEU d 144 " pdb=" CB LEU d 144 " pdb=" CD1 LEU d 144 " pdb=" CD2 LEU d 144 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB THR E 133 " pdb=" CA THR E 133 " pdb=" OG1 THR E 133 " pdb=" CG2 THR E 133 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.99e-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: 11.240 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 49.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.120 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 40216 Z= 0.158 Angle : 0.521 8.310 54875 Z= 0.283 Chirality : 0.040 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 aren 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 covalent geometry : bond 0.00342 (40215) covalent geometry : angle 0.52134 (54875) hydrogen bonds : bond 0.11229 ( 1968) hydrogen bonds : angle 5.10507 ( 5539) Misc. bond : bond 0.09037 ( 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 : 1.632 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: 0.2856 time to fit residues: 382.1986 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 : 1.459 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 301 GLN a 65 GLN a 293 ASN a 416 GLN d 21 GLN d 195 HIS e 21 GLN e 54 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.094960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.062227 restraints weight = 183953.000| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.36 r_work: 0.2797 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 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 = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 40216 Z= 0.165 Angle : 0.632 9.746 54875 Z= 0.332 Chirality : 0.042 0.241 6096 Planarity : 0.004 0.050 6532 Dihedral : 16.123 131.530 6508 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.02 % Allowed : 24.75 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.13), residues: 4454 helix: 2.37 (0.12), residues: 1760 sheet: 0.74 (0.19), residues: 732 loop : -0.35 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG e 153 TYR 0.025 0.001 TYR E 66 PHE 0.042 0.002 PHE E 180 TRP 0.026 0.001 TRP F 805 HIS 0.010 0.001 HIS c 89 Details of bonding type rmsd covalent geometry : bond 0.00380 (40215) covalent geometry : angle 0.63184 (54875) hydrogen bonds : bond 0.04540 ( 1968) hydrogen bonds : angle 4.53168 ( 5539) Misc. bond : bond 0.00209 ( 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 : 1.748 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: A 99 PHE cc_start: 0.8370 (m-10) cc_final: 0.8135 (m-10) REVERT: A 336 GLU cc_start: 0.8697 (tp30) cc_final: 0.8439 (tp30) REVERT: B 59 PHE cc_start: 0.8672 (p90) cc_final: 0.8259 (p90) REVERT: B 288 ASP cc_start: 0.8697 (t70) cc_final: 0.8383 (t0) REVERT: C 187 ASN cc_start: 0.9505 (m-40) cc_final: 0.8980 (m-40) REVERT: C 195 ILE cc_start: 0.9547 (tp) cc_final: 0.9304 (pt) REVERT: D 59 MET cc_start: 0.7408 (ppp) cc_final: 0.7086 (ppp) REVERT: D 151 LEU cc_start: 0.9709 (OUTLIER) cc_final: 0.9446 (mm) REVERT: D 162 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9216 (t80) REVERT: D 177 TYR cc_start: 0.8985 (m-80) cc_final: 0.8648 (m-80) REVERT: E 130 CYS cc_start: 0.9515 (m) cc_final: 0.9305 (p) REVERT: E 150 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8023 (tmm-80) REVERT: F 108 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8072 (tptt) REVERT: F 286 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8900 (t0) REVERT: F 354 MET cc_start: 0.6174 (tpt) cc_final: 0.5477 (tpt) REVERT: F 728 GLU cc_start: 0.9157 (mp0) cc_final: 0.8853 (mt-10) REVERT: F 746 MET cc_start: 0.8794 (mtp) cc_final: 0.8532 (mtp) REVERT: F 774 LEU cc_start: 0.9793 (tp) cc_final: 0.9424 (tp) REVERT: F 778 PHE cc_start: 0.9364 (m-80) cc_final: 0.8448 (m-80) REVERT: F 910 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8275 (mt) REVERT: G 191 LYS cc_start: 0.9172 (mttp) cc_final: 0.8946 (mttp) REVERT: a 158 GLN cc_start: 0.8903 (mp10) cc_final: 0.8701 (mp10) REVERT: a 199 PHE cc_start: 0.8612 (t80) cc_final: 0.8261 (t80) REVERT: a 516 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.9022 (mmtm) REVERT: b 14 MET cc_start: 0.8625 (ttt) cc_final: 0.8224 (tpp) REVERT: b 20 MET cc_start: 0.6505 (mtm) cc_final: 0.4027 (ttm) REVERT: b 127 PHE cc_start: 0.8142 (m-10) cc_final: 0.7850 (m-80) REVERT: b 292 GLU cc_start: 0.9078 (tt0) cc_final: 0.8549 (tp30) REVERT: c 42 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: c 215 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8489 (mm110) REVERT: d 18 HIS cc_start: 0.8307 (m170) cc_final: 0.6957 (m170) REVERT: d 21 GLN cc_start: 0.8911 (tt0) cc_final: 0.8654 (tm-30) REVERT: d 61 MET cc_start: 0.7128 (ttp) cc_final: 0.6314 (tmm) REVERT: d 132 ASP cc_start: 0.8959 (m-30) cc_final: 0.8759 (p0) REVERT: d 138 GLN cc_start: 0.9455 (tp40) cc_final: 0.8815 (tp-100) REVERT: d 172 LEU cc_start: 0.9733 (OUTLIER) cc_final: 0.9498 (pp) REVERT: e 4 LYS cc_start: 0.9372 (tppt) cc_final: 0.9155 (tptm) REVERT: e 21 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8266 (pp30) REVERT: e 125 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8876 (tm-30) REVERT: e 153 ARG cc_start: 0.9208 (ttp80) cc_final: 0.8943 (tmm160) REVERT: f 774 LEU cc_start: 0.9824 (OUTLIER) cc_final: 0.9572 (tt) REVERT: f 812 MET cc_start: 0.8697 (ppp) cc_final: 0.8268 (ppp) outliers start: 162 outliers final: 71 residues processed: 582 average time/residue: 0.2708 time to fit residues: 253.7074 Evaluate side-chains 458 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 376 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain A residue 427 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 91 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 369 ASP Chi-restraints excluded: chain B residue 471 ASP 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 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 271 GLU 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 666 VAL 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 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 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 435 VAL Chi-restraints excluded: chain a residue 506 LEU Chi-restraints excluded: chain a residue 516 LYS 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 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 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 89 SER 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 172 LEU Chi-restraints excluded: chain e residue 21 GLN Chi-restraints excluded: chain e residue 37 THR 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 774 LEU 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: 10.0000 chunk 196 optimal weight: 0.9990 chunk 389 optimal weight: 0.9980 chunk 411 optimal weight: 0.2980 chunk 201 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 421 optimal weight: 0.3980 chunk 342 optimal weight: 2.9990 chunk 374 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN C 62 ASN C 89 HIS E 54 GLN F 183 GLN c 215 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 = 0.3836 r_free = 0.3836 target = 0.095601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.062253 restraints weight = 172811.835| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 4.16 r_work: 0.2812 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 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 = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 40216 Z= 0.133 Angle : 0.582 13.278 54875 Z= 0.304 Chirality : 0.040 0.182 6096 Planarity : 0.004 0.049 6532 Dihedral : 16.068 130.138 6470 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.10 % Allowed : 24.45 % 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 aren not related in a simple way. whole: 1.38 (0.13), residues: 4454 helix: 2.36 (0.12), residues: 1743 sheet: 0.76 (0.19), residues: 731 loop : -0.33 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 71 TYR 0.018 0.001 TYR d 129 PHE 0.061 0.001 PHE E 180 TRP 0.038 0.001 TRP f 805 HIS 0.008 0.001 HIS d 18 Details of bonding type rmsd covalent geometry : bond 0.00297 (40215) covalent geometry : angle 0.58244 (54875) hydrogen bonds : bond 0.04185 ( 1968) hydrogen bonds : angle 4.38008 ( 5539) Misc. bond : bond 0.00044 ( 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 524 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 399 time to evaluate : 1.638 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: A 336 GLU cc_start: 0.8773 (tp30) cc_final: 0.8494 (tp30) REVERT: A 421 ASP cc_start: 0.8191 (t0) cc_final: 0.7947 (t0) REVERT: A 453 MET cc_start: 0.8843 (mmm) cc_final: 0.8430 (mmm) REVERT: B 14 MET cc_start: 0.8420 (mmm) cc_final: 0.8040 (mmp) REVERT: B 59 PHE cc_start: 0.8511 (p90) cc_final: 0.8111 (p90) REVERT: B 288 ASP cc_start: 0.8701 (t70) cc_final: 0.8371 (t0) REVERT: C 65 LEU cc_start: 0.9321 (tp) cc_final: 0.9088 (tp) REVERT: C 164 ILE cc_start: 0.8784 (tp) cc_final: 0.8458 (mm) REVERT: C 187 ASN cc_start: 0.9502 (m-40) cc_final: 0.8967 (m-40) REVERT: C 195 ILE cc_start: 0.9555 (tp) cc_final: 0.9264 (pt) REVERT: D 59 MET cc_start: 0.7307 (ppp) cc_final: 0.6970 (ppp) REVERT: D 150 ARG cc_start: 0.9212 (tmm-80) cc_final: 0.8789 (tmm-80) REVERT: D 162 PHE cc_start: 0.9379 (OUTLIER) cc_final: 0.9156 (t80) REVERT: D 176 LEU cc_start: 0.9553 (tt) cc_final: 0.9201 (pp) REVERT: D 177 TYR cc_start: 0.8945 (m-80) cc_final: 0.8291 (m-80) REVERT: E 130 CYS cc_start: 0.9546 (m) cc_final: 0.9324 (p) REVERT: E 150 ARG cc_start: 0.8798 (tmm-80) cc_final: 0.8096 (tmm-80) REVERT: F 95 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8604 (tm-30) REVERT: F 108 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8050 (tptt) REVERT: F 354 MET cc_start: 0.6161 (tpt) cc_final: 0.5497 (tpt) REVERT: F 728 GLU cc_start: 0.9178 (mp0) cc_final: 0.8868 (mt-10) REVERT: F 746 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8484 (mtp) REVERT: F 910 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8501 (mt) REVERT: a 158 GLN cc_start: 0.8868 (mp10) cc_final: 0.8668 (mp10) REVERT: a 199 PHE cc_start: 0.8559 (t80) cc_final: 0.8183 (t80) REVERT: a 346 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8503 (tpp) REVERT: a 423 GLN cc_start: 0.8964 (mp10) cc_final: 0.8718 (mp10) REVERT: b 14 MET cc_start: 0.8719 (ttt) cc_final: 0.8307 (tpp) REVERT: b 127 PHE cc_start: 0.7980 (m-10) cc_final: 0.7604 (m-80) REVERT: b 215 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7192 (mm) REVERT: b 306 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7732 (tp) REVERT: c 42 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: c 176 ARG cc_start: 0.7053 (ptt180) cc_final: 0.6849 (ptt180) REVERT: d 21 GLN cc_start: 0.9066 (tt0) cc_final: 0.8601 (tm-30) REVERT: d 59 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8717 (ttm) REVERT: d 61 MET cc_start: 0.7242 (ttp) cc_final: 0.6370 (tmm) REVERT: d 96 PHE cc_start: 0.9052 (p90) cc_final: 0.8766 (p90) REVERT: d 122 VAL cc_start: 0.8864 (t) cc_final: 0.8646 (p) REVERT: d 138 GLN cc_start: 0.9450 (tp40) cc_final: 0.8783 (tp-100) REVERT: d 172 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9521 (pp) REVERT: e 4 LYS cc_start: 0.9421 (tppt) cc_final: 0.9140 (tptm) REVERT: e 5 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8847 (mm) REVERT: e 58 ASP cc_start: 0.9028 (m-30) cc_final: 0.8535 (p0) REVERT: e 125 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8846 (tm-30) REVERT: e 153 ARG cc_start: 0.9227 (ttp80) cc_final: 0.8987 (tmm160) REVERT: f 743 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7623 (tmm) REVERT: f 774 LEU cc_start: 0.9834 (OUTLIER) cc_final: 0.9612 (tt) REVERT: f 812 MET cc_start: 0.8709 (ppp) cc_final: 0.8288 (ppp) outliers start: 125 outliers final: 64 residues processed: 499 average time/residue: 0.2541 time to fit residues: 206.5255 Evaluate side-chains 431 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 354 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 409 TYR Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE 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 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 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 123 ILE Chi-restraints excluded: chain D residue 130 CYS 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 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 307 THR Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 718 HIS Chi-restraints excluded: chain F residue 746 MET 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 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 312 LEU Chi-restraints excluded: chain a residue 346 MET 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 13 CYS 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 41 LEU 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 d residue 9 HIS Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 33 VAL Chi-restraints excluded: chain d residue 59 MET 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 e residue 5 ILE Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain e residue 189 THR Chi-restraints excluded: chain f residue 662 VAL Chi-restraints excluded: chain f residue 743 MET Chi-restraints excluded: chain f residue 774 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 346 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 327 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 chunk 345 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 410 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 414 HIS e 21 GLN f 862 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.094673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060505 restraints weight = 207729.138| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.59 r_work: 0.2767 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 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 = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2762 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= 0.159 Angle : 0.571 13.426 54875 Z= 0.298 Chirality : 0.040 0.304 6096 Planarity : 0.004 0.051 6532 Dihedral : 16.124 130.001 6464 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.50 % Allowed : 24.01 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.13), residues: 4454 helix: 2.37 (0.12), residues: 1744 sheet: 0.77 (0.19), residues: 733 loop : -0.30 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.022 0.001 TYR d 129 PHE 0.056 0.001 PHE E 180 TRP 0.026 0.001 TRP f 805 HIS 0.007 0.001 HIS b 414 Details of bonding type rmsd covalent geometry : bond 0.00364 (40215) covalent geometry : angle 0.57116 (54875) hydrogen bonds : bond 0.04098 ( 1968) hydrogen bonds : angle 4.32367 ( 5539) Misc. bond : bond 0.00076 ( 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 524 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 383 time to evaluate : 1.651 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 336 GLU cc_start: 0.8899 (tp30) cc_final: 0.8648 (tp30) REVERT: A 421 ASP cc_start: 0.8181 (t0) cc_final: 0.7869 (t0) REVERT: A 453 MET cc_start: 0.8893 (mmm) cc_final: 0.8492 (mmm) REVERT: B 288 ASP cc_start: 0.8718 (t70) cc_final: 0.8362 (t0) REVERT: B 452 ASN cc_start: 0.8881 (m-40) cc_final: 0.8618 (m-40) REVERT: C 187 ASN cc_start: 0.9514 (m-40) cc_final: 0.8987 (m-40) REVERT: C 195 ILE cc_start: 0.9568 (tp) cc_final: 0.9236 (pt) REVERT: D 59 MET cc_start: 0.7554 (ppp) cc_final: 0.7009 (ppp) REVERT: D 150 ARG cc_start: 0.9291 (tmm-80) cc_final: 0.8912 (tmm-80) REVERT: D 176 LEU cc_start: 0.9559 (OUTLIER) cc_final: 0.9150 (pp) REVERT: D 177 TYR cc_start: 0.9005 (m-80) cc_final: 0.8351 (m-80) REVERT: E 1 MET cc_start: 0.9123 (mmm) cc_final: 0.8842 (tpt) REVERT: E 150 ARG cc_start: 0.8915 (tmm-80) cc_final: 0.8335 (tmm-80) REVERT: E 157 ASP cc_start: 0.9477 (m-30) cc_final: 0.8984 (t0) REVERT: F 95 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8714 (tm-30) REVERT: F 108 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8055 (tptt) REVERT: F 286 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8904 (t0) REVERT: F 354 MET cc_start: 0.6145 (tpt) cc_final: 0.5450 (tpt) REVERT: F 725 TRP cc_start: 0.8895 (t60) cc_final: 0.8538 (t60) REVERT: F 728 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8874 (mt-10) REVERT: F 746 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8432 (mtp) REVERT: F 778 PHE cc_start: 0.9273 (m-80) cc_final: 0.8453 (m-80) REVERT: a 135 MET cc_start: 0.8864 (mmt) cc_final: 0.8535 (mmt) REVERT: a 199 PHE cc_start: 0.8621 (t80) cc_final: 0.8266 (t80) REVERT: a 358 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9095 (ttpt) REVERT: a 533 ASP cc_start: 0.9135 (OUTLIER) cc_final: 0.8934 (p0) REVERT: b 14 MET cc_start: 0.8747 (ttt) cc_final: 0.8444 (tpp) REVERT: b 127 PHE cc_start: 0.8097 (m-10) cc_final: 0.7678 (m-80) REVERT: b 215 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7228 (mm) REVERT: b 292 GLU cc_start: 0.8969 (tt0) cc_final: 0.8482 (tp30) REVERT: b 306 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7818 (tp) REVERT: c 42 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: c 50 ASP cc_start: 0.7731 (p0) cc_final: 0.7515 (p0) REVERT: c 85 LYS cc_start: 0.9249 (ttmt) cc_final: 0.8965 (mttt) REVERT: c 176 ARG cc_start: 0.7037 (ptt180) cc_final: 0.6827 (ptt180) REVERT: d 58 ASP cc_start: 0.9745 (m-30) cc_final: 0.9436 (p0) REVERT: d 61 MET cc_start: 0.7388 (ttp) cc_final: 0.7177 (tmm) REVERT: d 96 PHE cc_start: 0.9059 (p90) cc_final: 0.8699 (p90) REVERT: d 138 GLN cc_start: 0.9457 (tp40) cc_final: 0.8943 (tm-30) REVERT: d 172 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9527 (pp) REVERT: d 192 ARG cc_start: 0.9139 (tpp80) cc_final: 0.8623 (mmm160) REVERT: e 59 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8452 (mmm) REVERT: e 153 ARG cc_start: 0.9245 (ttp80) cc_final: 0.8978 (tmm160) REVERT: e 181 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9459 (tp) REVERT: f 698 TYR cc_start: 0.8957 (t80) cc_final: 0.8647 (t80) REVERT: f 739 GLN cc_start: 0.8623 (mp10) cc_final: 0.8420 (mp10) REVERT: f 743 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7614 (tmm) REVERT: f 761 TYR cc_start: 0.9312 (m-10) cc_final: 0.9030 (m-80) REVERT: f 774 LEU cc_start: 0.9840 (OUTLIER) cc_final: 0.9584 (mt) REVERT: f 812 MET cc_start: 0.8716 (ppp) cc_final: 0.8238 (ppp) outliers start: 141 outliers final: 76 residues processed: 493 average time/residue: 0.2597 time to fit residues: 207.2354 Evaluate side-chains 443 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 353 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 281 LEU 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 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 123 ILE Chi-restraints excluded: chain D residue 130 CYS 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 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 286 ASP Chi-restraints excluded: chain F residue 360 LEU Chi-restraints excluded: chain F residue 394 THR Chi-restraints excluded: chain F residue 476 ARG 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 746 MET Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 756 ARG Chi-restraints excluded: chain F residue 771 LEU 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 242 LEU Chi-restraints excluded: chain a residue 312 LEU 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 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 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 41 LEU Chi-restraints excluded: chain c residue 42 GLN Chi-restraints excluded: chain c residue 65 LEU 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 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 130 CYS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 158 VAL 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 59 MET Chi-restraints excluded: chain e residue 181 ILE 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 774 LEU Chi-restraints excluded: chain f residue 781 ILE 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: 0.9990 chunk 421 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 440 optimal weight: 9.9990 chunk 427 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 369 optimal weight: 0.0970 chunk 262 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 119 optimal weight: 0.0020 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.094826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061363 restraints weight = 163716.552| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.07 r_work: 0.2798 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40216 Z= 0.136 Angle : 0.565 13.741 54875 Z= 0.293 Chirality : 0.040 0.322 6096 Planarity : 0.004 0.051 6532 Dihedral : 16.122 129.266 6456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.12 % Allowed : 24.40 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.13), residues: 4454 helix: 2.38 (0.12), residues: 1742 sheet: 0.81 (0.19), residues: 743 loop : -0.31 (0.14), residues: 1969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 71 TYR 0.023 0.001 TYR d 129 PHE 0.058 0.001 PHE E 180 TRP 0.025 0.001 TRP f 805 HIS 0.005 0.001 HIS f 862 Details of bonding type rmsd covalent geometry : bond 0.00308 (40215) covalent geometry : angle 0.56493 (54875) hydrogen bonds : bond 0.03951 ( 1968) hydrogen bonds : angle 4.23982 ( 5539) Misc. bond : bond 0.00049 ( 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 500 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 374 time to evaluate : 1.651 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 185 ARG cc_start: 0.9183 (mmm160) cc_final: 0.8921 (mmm160) REVERT: A 336 GLU cc_start: 0.8856 (tp30) cc_final: 0.8584 (tp30) REVERT: A 421 ASP cc_start: 0.8191 (t0) cc_final: 0.7895 (t0) REVERT: A 453 MET cc_start: 0.8873 (mmm) cc_final: 0.8472 (mmm) REVERT: B 288 ASP cc_start: 0.8648 (t70) cc_final: 0.8299 (t0) REVERT: B 452 ASN cc_start: 0.8872 (m-40) cc_final: 0.8603 (m-40) REVERT: D 59 MET cc_start: 0.7530 (ppp) cc_final: 0.6996 (ppp) REVERT: D 150 ARG cc_start: 0.9307 (tmm-80) cc_final: 0.8836 (tmm-80) REVERT: D 176 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9260 (pp) REVERT: D 177 TYR cc_start: 0.9087 (m-80) cc_final: 0.8413 (m-80) REVERT: D 194 LEU cc_start: 0.9002 (tp) cc_final: 0.8614 (tp) REVERT: E 150 ARG cc_start: 0.8960 (tmm-80) cc_final: 0.8512 (tmm-80) REVERT: E 157 ASP cc_start: 0.9401 (m-30) cc_final: 0.8845 (t0) REVERT: F 95 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8701 (tm-30) REVERT: F 108 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8059 (tptt) REVERT: F 286 ASP cc_start: 0.9231 (OUTLIER) cc_final: 0.8877 (t0) REVERT: F 308 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: F 354 MET cc_start: 0.6076 (tpt) cc_final: 0.5329 (tpt) REVERT: F 616 TYR cc_start: 0.8072 (m-80) cc_final: 0.7848 (m-80) REVERT: F 725 TRP cc_start: 0.8878 (t60) cc_final: 0.8577 (t60) REVERT: F 728 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8851 (mt-10) REVERT: F 746 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8601 (mtp) REVERT: F 756 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9054 (mpp80) REVERT: F 910 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8527 (mt) REVERT: G 191 LYS cc_start: 0.9203 (mttp) cc_final: 0.8990 (pttm) REVERT: a 135 MET cc_start: 0.8965 (mmt) cc_final: 0.8559 (mmt) REVERT: a 199 PHE cc_start: 0.8615 (t80) cc_final: 0.8299 (t80) REVERT: a 358 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9108 (ttpt) REVERT: a 533 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8916 (p0) REVERT: b 14 MET cc_start: 0.8739 (ttt) cc_final: 0.8432 (tpp) REVERT: b 127 PHE cc_start: 0.8109 (m-10) cc_final: 0.7679 (m-80) REVERT: b 215 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7212 (mm) REVERT: b 277 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8215 (p) REVERT: b 292 GLU cc_start: 0.8969 (tt0) cc_final: 0.8473 (tp30) REVERT: b 306 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7831 (tp) REVERT: c 50 ASP cc_start: 0.7643 (p0) cc_final: 0.7433 (p0) REVERT: c 167 TYR cc_start: 0.7290 (t80) cc_final: 0.7080 (t80) REVERT: d 58 ASP cc_start: 0.9747 (m-30) cc_final: 0.9456 (p0) REVERT: d 61 MET cc_start: 0.7941 (ttp) cc_final: 0.6919 (tmm) REVERT: d 96 PHE cc_start: 0.9043 (p90) cc_final: 0.8658 (p90) REVERT: d 138 GLN cc_start: 0.9445 (tp40) cc_final: 0.8941 (tm-30) REVERT: d 172 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9538 (pp) REVERT: d 192 ARG cc_start: 0.9143 (tpp80) cc_final: 0.8585 (mmm160) REVERT: e 4 LYS cc_start: 0.9415 (tppt) cc_final: 0.9178 (tptm) REVERT: e 59 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: e 153 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8982 (tmm160) REVERT: f 698 TYR cc_start: 0.8928 (t80) cc_final: 0.8623 (t80) REVERT: f 739 GLN cc_start: 0.8804 (mp10) cc_final: 0.8500 (mp10) REVERT: f 761 TYR cc_start: 0.9261 (m-10) cc_final: 0.9030 (m-80) REVERT: f 774 LEU cc_start: 0.9839 (OUTLIER) cc_final: 0.9618 (tt) REVERT: f 812 MET cc_start: 0.8712 (ppp) cc_final: 0.7973 (ppp) outliers start: 126 outliers final: 82 residues processed: 472 average time/residue: 0.2559 time to fit residues: 197.1176 Evaluate side-chains 449 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 352 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 95 ASN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 MET 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 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 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 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 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 746 MET Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 756 ARG 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 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 358 LYS 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 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 41 LEU 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 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 172 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 59 MET 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: 4.9990 chunk 163 optimal weight: 0.9990 chunk 317 optimal weight: 0.6980 chunk 313 optimal weight: 0.9990 chunk 222 optimal weight: 0.0050 chunk 38 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 426 optimal weight: 7.9990 chunk 397 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 390 optimal weight: 3.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 101 ASN C 48 GLN C 75 HIS d 21 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.094753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061625 restraints weight = 177419.234| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 4.16 r_work: 0.2804 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 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 = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 40216 Z= 0.123 Angle : 0.558 11.923 54875 Z= 0.289 Chirality : 0.040 0.271 6096 Planarity : 0.003 0.052 6532 Dihedral : 16.091 128.380 6454 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.22 % Allowed : 24.08 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.13), residues: 4454 helix: 2.39 (0.13), residues: 1743 sheet: 0.84 (0.19), residues: 743 loop : -0.31 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG e 161 TYR 0.022 0.001 TYR d 129 PHE 0.036 0.001 PHE F 813 TRP 0.024 0.001 TRP f 805 HIS 0.004 0.001 HIS d 18 Details of bonding type rmsd covalent geometry : bond 0.00274 (40215) covalent geometry : angle 0.55834 (54875) hydrogen bonds : bond 0.03808 ( 1968) hydrogen bonds : angle 4.19054 ( 5539) Misc. bond : bond 0.00024 ( 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 512 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 382 time to evaluate : 1.667 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: A 161 MET cc_start: 0.8796 (mmt) cc_final: 0.8572 (mmt) REVERT: A 185 ARG cc_start: 0.9191 (mmm160) cc_final: 0.8930 (mmm160) REVERT: A 336 GLU cc_start: 0.8848 (tp30) cc_final: 0.8567 (tp30) REVERT: A 421 ASP cc_start: 0.8162 (t0) cc_final: 0.7869 (t0) REVERT: A 453 MET cc_start: 0.8860 (mmm) cc_final: 0.8448 (mmm) REVERT: B 14 MET cc_start: 0.8471 (mmm) cc_final: 0.8215 (mmm) REVERT: B 452 ASN cc_start: 0.8871 (m-40) cc_final: 0.8609 (m-40) REVERT: C 195 ILE cc_start: 0.9517 (tp) cc_final: 0.9295 (pt) REVERT: C 212 MET cc_start: 0.8943 (mpp) cc_final: 0.8585 (mpp) REVERT: D 59 MET cc_start: 0.7502 (ppp) cc_final: 0.6897 (ppp) REVERT: D 150 ARG cc_start: 0.9335 (tmm-80) cc_final: 0.9122 (tmm-80) REVERT: D 176 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9205 (pp) REVERT: D 177 TYR cc_start: 0.9072 (m-80) cc_final: 0.8371 (m-80) REVERT: E 150 ARG cc_start: 0.9001 (tmm-80) cc_final: 0.8532 (tmm-80) REVERT: E 157 ASP cc_start: 0.9409 (m-30) cc_final: 0.8825 (t0) REVERT: F 95 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8723 (tm-30) REVERT: F 108 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8066 (tptt) REVERT: F 286 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8876 (t0) REVERT: F 308 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8363 (pm20) REVERT: F 354 MET cc_start: 0.6147 (tpt) cc_final: 0.5392 (tpt) REVERT: F 616 TYR cc_start: 0.8124 (m-80) cc_final: 0.7896 (m-80) REVERT: F 725 TRP cc_start: 0.8857 (t60) cc_final: 0.8483 (t60) REVERT: F 728 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8846 (mt-10) REVERT: F 746 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: F 756 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.9033 (mpp80) REVERT: F 778 PHE cc_start: 0.9239 (m-80) cc_final: 0.8421 (m-80) REVERT: a 134 MET cc_start: 0.9152 (tmm) cc_final: 0.8841 (tmm) REVERT: a 135 MET cc_start: 0.9000 (mmt) cc_final: 0.8348 (mmt) REVERT: a 199 PHE cc_start: 0.8650 (t80) cc_final: 0.8370 (t80) REVERT: a 533 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8883 (p0) REVERT: b 14 MET cc_start: 0.8740 (ttt) cc_final: 0.8369 (tpp) REVERT: b 20 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6194 (ptm) REVERT: b 127 PHE cc_start: 0.8136 (m-10) cc_final: 0.7711 (m-80) REVERT: b 215 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7247 (mm) REVERT: b 277 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8253 (p) REVERT: b 292 GLU cc_start: 0.8992 (tt0) cc_final: 0.8578 (tp30) REVERT: b 306 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7904 (tp) REVERT: c 1 MET cc_start: 0.8417 (pmm) cc_final: 0.8006 (ppp) REVERT: c 50 ASP cc_start: 0.7628 (p0) cc_final: 0.7420 (p0) REVERT: c 167 TYR cc_start: 0.7327 (t80) cc_final: 0.7105 (t80) REVERT: d 58 ASP cc_start: 0.9742 (m-30) cc_final: 0.9487 (p0) REVERT: d 61 MET cc_start: 0.7914 (ttp) cc_final: 0.6832 (tmm) REVERT: d 96 PHE cc_start: 0.9026 (p90) cc_final: 0.8604 (p90) REVERT: d 138 GLN cc_start: 0.9429 (tp40) cc_final: 0.8906 (tm-30) REVERT: d 172 LEU cc_start: 0.9768 (OUTLIER) cc_final: 0.9542 (pp) REVERT: d 192 ARG cc_start: 0.9154 (tpp80) cc_final: 0.8927 (mmm160) REVERT: e 4 LYS cc_start: 0.9422 (tppt) cc_final: 0.9131 (tptm) REVERT: e 59 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8469 (mmm) REVERT: e 89 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8426 (p) REVERT: e 153 ARG cc_start: 0.9242 (ttp80) cc_final: 0.8971 (tmm160) REVERT: f 698 TYR cc_start: 0.8923 (t80) cc_final: 0.8621 (t80) REVERT: f 735 PHE cc_start: 0.8225 (t80) cc_final: 0.7859 (t80) REVERT: f 761 TYR cc_start: 0.9194 (m-10) cc_final: 0.8917 (m-80) REVERT: f 774 LEU cc_start: 0.9834 (OUTLIER) cc_final: 0.9462 (tp) REVERT: f 812 MET cc_start: 0.8787 (ppp) cc_final: 0.7975 (ppp) outliers start: 130 outliers final: 80 residues processed: 484 average time/residue: 0.2524 time to fit residues: 199.9830 Evaluate side-chains 453 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 358 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 75 ILE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 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 436 SER 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 C residue 182 GLU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 130 CYS 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 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 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 746 MET Chi-restraints excluded: chain F residue 747 CYS Chi-restraints excluded: chain F residue 756 ARG Chi-restraints excluded: chain F residue 771 LEU Chi-restraints excluded: chain F residue 840 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 242 LEU Chi-restraints excluded: chain a residue 409 TYR 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 41 LEU 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 d residue 59 MET Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 148 ASN 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 59 MET Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 89 SER 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 Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 110 optimal weight: 0.8980 chunk 387 optimal weight: 0.7980 chunk 437 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 337 optimal weight: 4.9990 chunk 444 optimal weight: 5.9990 chunk 428 optimal weight: 0.8980 chunk 302 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.094312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.061018 restraints weight = 178984.599| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 4.18 r_work: 0.2794 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3227 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= 0.141 Angle : 0.570 13.986 54875 Z= 0.293 Chirality : 0.040 0.250 6096 Planarity : 0.003 0.052 6532 Dihedral : 16.126 128.421 6453 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.03 % Allowed : 24.70 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.13), residues: 4454 helix: 2.33 (0.12), residues: 1744 sheet: 0.84 (0.19), residues: 745 loop : -0.30 (0.14), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 161 TYR 0.024 0.001 TYR d 129 PHE 0.064 0.001 PHE E 180 TRP 0.027 0.001 TRP F 893 HIS 0.018 0.001 HIS d 18 Details of bonding type rmsd covalent geometry : bond 0.00321 (40215) covalent geometry : angle 0.56988 (54875) hydrogen bonds : bond 0.03824 ( 1968) hydrogen bonds : angle 4.19509 ( 5539) Misc. bond : bond 0.00050 ( 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 500 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 378 time to evaluate : 1.725 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 185 ARG cc_start: 0.9222 (mmm160) cc_final: 0.8955 (mmm160) REVERT: A 336 GLU cc_start: 0.8854 (tp30) cc_final: 0.8568 (tp30) REVERT: A 421 ASP cc_start: 0.8148 (t0) cc_final: 0.7860 (t0) REVERT: A 453 MET cc_start: 0.8853 (mmm) cc_final: 0.8446 (mmm) REVERT: B 210 MET cc_start: 0.9514 (tmm) cc_final: 0.9090 (ptp) REVERT: B 452 ASN cc_start: 0.8882 (m-40) cc_final: 0.8595 (m-40) REVERT: C 195 ILE cc_start: 0.9514 (tp) cc_final: 0.9250 (pt) REVERT: D 59 MET cc_start: 0.7580 (ppp) cc_final: 0.6951 (ppp) REVERT: D 150 ARG cc_start: 0.9357 (tmm-80) cc_final: 0.8995 (tmm-80) REVERT: D 176 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9277 (pp) REVERT: D 177 TYR cc_start: 0.9098 (m-80) cc_final: 0.8517 (m-80) REVERT: E 61 MET cc_start: 0.7449 (tmm) cc_final: 0.7243 (tmm) REVERT: E 150 ARG cc_start: 0.9035 (tmm-80) cc_final: 0.8548 (tmm-80) REVERT: E 157 ASP cc_start: 0.9394 (m-30) cc_final: 0.8678 (t0) REVERT: E 161 ARG cc_start: 0.9268 (mmp80) cc_final: 0.9046 (mmp80) REVERT: F 95 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8748 (tm-30) REVERT: F 108 LYS cc_start: 0.8679 (ttpt) cc_final: 0.8081 (tptt) REVERT: F 286 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8865 (t0) REVERT: F 308 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8377 (pm20) REVERT: F 354 MET cc_start: 0.6119 (tpt) cc_final: 0.5386 (tpt) REVERT: F 616 TYR cc_start: 0.8138 (m-80) cc_final: 0.7893 (m-80) REVERT: F 725 TRP cc_start: 0.8855 (t60) cc_final: 0.8494 (t60) REVERT: F 728 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8870 (mt-10) REVERT: F 746 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8483 (mtp) REVERT: F 910 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8588 (mt) REVERT: a 134 MET cc_start: 0.9153 (tmm) cc_final: 0.8835 (tmm) REVERT: a 135 MET cc_start: 0.9026 (mmt) cc_final: 0.8403 (mmt) REVERT: a 199 PHE cc_start: 0.8660 (t80) cc_final: 0.8390 (t80) REVERT: a 358 LYS cc_start: 0.9404 (OUTLIER) cc_final: 0.9082 (ttpt) REVERT: a 533 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8897 (p0) REVERT: b 14 MET cc_start: 0.8754 (ttt) cc_final: 0.8168 (tpp) REVERT: b 20 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6208 (ptm) REVERT: b 99 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8385 (mm-40) REVERT: b 127 PHE cc_start: 0.8164 (m-10) cc_final: 0.7744 (m-80) REVERT: b 215 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7229 (mm) REVERT: b 277 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8283 (p) REVERT: b 292 GLU cc_start: 0.8869 (tt0) cc_final: 0.8525 (tp30) REVERT: b 306 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7914 (tp) REVERT: c 167 TYR cc_start: 0.7368 (t80) cc_final: 0.7110 (t80) REVERT: d 61 MET cc_start: 0.7918 (ttp) cc_final: 0.6829 (tmm) REVERT: d 96 PHE cc_start: 0.9031 (p90) cc_final: 0.8585 (p90) REVERT: d 138 GLN cc_start: 0.9422 (tp40) cc_final: 0.8894 (tm-30) REVERT: d 172 LEU cc_start: 0.9775 (OUTLIER) cc_final: 0.9564 (pp) REVERT: d 192 ARG cc_start: 0.9158 (tpp80) cc_final: 0.8915 (mmm160) REVERT: e 4 LYS cc_start: 0.9432 (tppt) cc_final: 0.9098 (tptm) REVERT: e 59 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8544 (mmm) REVERT: e 89 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8421 (p) REVERT: e 153 ARG cc_start: 0.9219 (ttp80) cc_final: 0.8950 (tmm160) REVERT: f 698 TYR cc_start: 0.8916 (t80) cc_final: 0.8572 (t80) REVERT: f 735 PHE cc_start: 0.8235 (t80) cc_final: 0.7817 (t80) REVERT: f 774 LEU cc_start: 0.9835 (OUTLIER) cc_final: 0.9634 (tt) REVERT: f 812 MET cc_start: 0.8810 (ppp) cc_final: 0.7983 (ppp) outliers start: 122 outliers final: 83 residues processed: 468 average time/residue: 0.2547 time to fit residues: 194.6973 Evaluate side-chains 456 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 356 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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 95 ASN Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 409 TYR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 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 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 164 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 130 CYS 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 106 PHE 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 746 MET 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 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 206 LYS Chi-restraints excluded: chain a residue 358 LYS 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 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 41 LEU 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 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 172 LEU Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 59 MET Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 89 SER 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 Chi-restraints excluded: chain f residue 845 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 353 optimal weight: 3.9990 chunk 338 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 354 optimal weight: 0.8980 chunk 260 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 442 optimal weight: 4.9990 chunk 426 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN b 414 HIS d 21 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 = 0.3808 r_free = 0.3808 target = 0.093509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060051 restraints weight = 177660.203| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.14 r_work: 0.2768 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40216 Z= 0.182 Angle : 0.592 15.374 54875 Z= 0.304 Chirality : 0.041 0.233 6096 Planarity : 0.004 0.054 6532 Dihedral : 16.231 129.001 6453 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.05 % Allowed : 24.75 % 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 aren not related in a simple way. whole: 1.35 (0.13), residues: 4454 helix: 2.29 (0.12), residues: 1745 sheet: 0.78 (0.19), residues: 733 loop : -0.31 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 161 TYR 0.023 0.001 TYR d 129 PHE 0.065 0.001 PHE E 180 TRP 0.022 0.001 TRP f 805 HIS 0.006 0.001 HIS b 414 Details of bonding type rmsd covalent geometry : bond 0.00420 (40215) covalent geometry : angle 0.59214 (54875) hydrogen bonds : bond 0.03992 ( 1968) hydrogen bonds : angle 4.24648 ( 5539) Misc. bond : bond 0.00088 ( 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 485 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 362 time to evaluate : 1.746 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: A 185 ARG cc_start: 0.9241 (mmm160) cc_final: 0.8992 (mmm160) REVERT: A 336 GLU cc_start: 0.8884 (tp30) cc_final: 0.8615 (tp30) REVERT: A 421 ASP cc_start: 0.8146 (t0) cc_final: 0.7853 (t0) REVERT: A 453 MET cc_start: 0.8882 (mmm) cc_final: 0.8539 (mmm) REVERT: B 14 MET cc_start: 0.8427 (mmm) cc_final: 0.7985 (mmp) REVERT: B 210 MET cc_start: 0.9524 (tmm) cc_final: 0.9128 (ptp) REVERT: B 452 ASN cc_start: 0.8902 (m-40) cc_final: 0.8612 (m-40) REVERT: C 195 ILE cc_start: 0.9535 (tp) cc_final: 0.9240 (pt) REVERT: D 59 MET cc_start: 0.7619 (ppp) cc_final: 0.6960 (ppp) REVERT: D 150 ARG cc_start: 0.9363 (tmm-80) cc_final: 0.9060 (tmm-80) REVERT: D 176 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9242 (pp) REVERT: D 177 TYR cc_start: 0.9156 (m-80) cc_final: 0.8556 (m-80) REVERT: E 150 ARG cc_start: 0.9029 (tmm-80) cc_final: 0.8436 (tmm-80) REVERT: F 95 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8790 (tm-30) REVERT: F 108 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8094 (tptt) REVERT: F 121 ASP cc_start: 0.8517 (m-30) cc_final: 0.8267 (m-30) REVERT: F 286 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8858 (t0) REVERT: F 308 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8384 (pm20) REVERT: F 616 TYR cc_start: 0.8158 (m-80) cc_final: 0.7914 (m-80) REVERT: F 725 TRP cc_start: 0.8899 (t60) cc_final: 0.8539 (t60) REVERT: F 728 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8888 (mt-10) REVERT: F 746 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8470 (mtp) REVERT: F 778 PHE cc_start: 0.9236 (m-80) cc_final: 0.8443 (m-80) REVERT: F 910 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8579 (mt) REVERT: a 134 MET cc_start: 0.9144 (tmm) cc_final: 0.8819 (tmm) REVERT: a 135 MET cc_start: 0.9053 (mmt) cc_final: 0.8433 (mmt) REVERT: a 199 PHE cc_start: 0.8699 (t80) cc_final: 0.8453 (t80) REVERT: a 358 LYS cc_start: 0.9424 (OUTLIER) cc_final: 0.9100 (ttpt) REVERT: b 14 MET cc_start: 0.8686 (ttt) cc_final: 0.8251 (tpp) REVERT: b 20 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6212 (ptm) REVERT: b 99 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8378 (mm-40) REVERT: b 127 PHE cc_start: 0.8184 (m-80) cc_final: 0.7742 (m-80) REVERT: b 215 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7241 (mm) REVERT: b 277 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8267 (p) REVERT: b 292 GLU cc_start: 0.8913 (tt0) cc_final: 0.8541 (tp30) REVERT: b 306 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8004 (tp) REVERT: c 42 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: c 50 ASP cc_start: 0.7709 (p0) cc_final: 0.7496 (p0) REVERT: c 85 LYS cc_start: 0.9236 (ttmt) cc_final: 0.9002 (mttt) REVERT: c 167 TYR cc_start: 0.7484 (t80) cc_final: 0.7235 (t80) REVERT: d 21 GLN cc_start: 0.9063 (tt0) cc_final: 0.8609 (tm-30) REVERT: d 59 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8703 (ttp) REVERT: d 61 MET cc_start: 0.8167 (ttp) cc_final: 0.7117 (tmm) REVERT: d 96 PHE cc_start: 0.9030 (p90) cc_final: 0.8585 (p90) REVERT: d 138 GLN cc_start: 0.9412 (tp40) cc_final: 0.8865 (tm-30) REVERT: d 172 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9570 (pp) REVERT: d 192 ARG cc_start: 0.9160 (tpp80) cc_final: 0.8907 (mmm160) REVERT: e 59 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8575 (mmm) REVERT: e 89 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8393 (p) REVERT: e 153 ARG cc_start: 0.9222 (ttp80) cc_final: 0.8955 (tmm160) REVERT: f 698 TYR cc_start: 0.8946 (t80) cc_final: 0.8664 (t80) REVERT: f 735 PHE cc_start: 0.8290 (t80) cc_final: 0.7894 (t80) outliers start: 123 outliers final: 83 residues processed: 453 average time/residue: 0.2500 time to fit residues: 186.2710 Evaluate side-chains 451 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 351 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 95 ASN 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 420 LEU 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 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 164 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 130 CYS 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 106 PHE 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 324 GLN 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 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 746 MET 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 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 358 LYS 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 13 CYS 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 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 41 LEU 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 59 MET Chi-restraints excluded: chain d residue 74 LEU Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain e residue 21 GLN Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 59 MET Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 170 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 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: 4.9990 chunk 416 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 305 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 294 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 421 optimal weight: 5.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 95 ASN 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 = 0.3805 r_free = 0.3805 target = 0.093338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060027 restraints weight = 165913.637| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.01 r_work: 0.2772 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 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 = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 40216 Z= 0.179 Angle : 0.613 14.245 54875 Z= 0.313 Chirality : 0.041 0.316 6096 Planarity : 0.004 0.060 6532 Dihedral : 16.290 128.915 6453 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.78 % Allowed : 25.45 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.13), residues: 4454 helix: 2.25 (0.13), residues: 1745 sheet: 0.75 (0.19), residues: 742 loop : -0.32 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG d 161 TYR 0.025 0.001 TYR d 129 PHE 0.068 0.001 PHE E 180 TRP 0.022 0.001 TRP f 805 HIS 0.004 0.001 HIS F 482 Details of bonding type rmsd covalent geometry : bond 0.00414 (40215) covalent geometry : angle 0.61287 (54875) hydrogen bonds : bond 0.03981 ( 1968) hydrogen bonds : angle 4.27930 ( 5539) Misc. bond : bond 0.00091 ( 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 462 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 350 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8759 (ptt90) REVERT: A 185 ARG cc_start: 0.9242 (mmm160) cc_final: 0.8996 (mmm160) REVERT: A 421 ASP cc_start: 0.8173 (t0) cc_final: 0.7878 (t0) REVERT: A 453 MET cc_start: 0.8886 (mmm) cc_final: 0.8557 (mmm) REVERT: B 14 MET cc_start: 0.8459 (mmm) cc_final: 0.7955 (mmp) REVERT: B 210 MET cc_start: 0.9528 (tmm) cc_final: 0.9144 (ptp) REVERT: B 436 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 452 ASN cc_start: 0.8902 (m-40) cc_final: 0.8625 (m110) REVERT: C 195 ILE cc_start: 0.9540 (tp) cc_final: 0.9234 (pt) REVERT: D 59 MET cc_start: 0.7608 (ppp) cc_final: 0.6906 (ppp) REVERT: D 150 ARG cc_start: 0.9345 (tmm-80) cc_final: 0.9061 (tmm-80) REVERT: D 176 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9244 (pp) REVERT: D 177 TYR cc_start: 0.9148 (m-80) cc_final: 0.8547 (m-80) REVERT: E 150 ARG cc_start: 0.9035 (tmm-80) cc_final: 0.8414 (tmm-80) REVERT: F 95 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8781 (tm-30) REVERT: F 108 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8094 (tptt) REVERT: F 121 ASP cc_start: 0.8516 (m-30) cc_final: 0.8269 (m-30) REVERT: F 286 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8847 (t0) REVERT: F 308 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8478 (pm20) REVERT: F 616 TYR cc_start: 0.8147 (m-80) cc_final: 0.7885 (m-80) REVERT: F 725 TRP cc_start: 0.8913 (t60) cc_final: 0.8555 (t60) REVERT: F 728 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8888 (mt-10) REVERT: F 746 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8464 (mtp) REVERT: F 778 PHE cc_start: 0.9199 (m-80) cc_final: 0.8419 (m-80) REVERT: F 910 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8610 (mt) REVERT: a 134 MET cc_start: 0.9129 (tmm) cc_final: 0.8808 (tmm) REVERT: a 135 MET cc_start: 0.9043 (mmt) cc_final: 0.8456 (mmt) REVERT: a 199 PHE cc_start: 0.8644 (t80) cc_final: 0.8417 (t80) REVERT: a 358 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9104 (ttpt) REVERT: b 14 MET cc_start: 0.8650 (ttt) cc_final: 0.8206 (tpp) REVERT: b 20 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6214 (ptm) REVERT: b 99 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (mm-40) REVERT: b 127 PHE cc_start: 0.8240 (m-80) cc_final: 0.7802 (m-80) REVERT: b 215 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7268 (mm) REVERT: b 277 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8274 (p) REVERT: b 306 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7997 (tp) REVERT: c 42 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8439 (mp10) REVERT: c 167 TYR cc_start: 0.7487 (t80) cc_final: 0.7244 (t80) REVERT: d 59 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8713 (ttp) REVERT: d 61 MET cc_start: 0.8130 (ttp) cc_final: 0.7109 (tmm) REVERT: d 96 PHE cc_start: 0.8982 (p90) cc_final: 0.8513 (p90) REVERT: d 138 GLN cc_start: 0.9441 (tp40) cc_final: 0.8873 (tm-30) REVERT: d 172 LEU cc_start: 0.9758 (OUTLIER) cc_final: 0.9547 (pp) REVERT: d 192 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8933 (mmm160) REVERT: e 59 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8584 (mmm) REVERT: e 89 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8372 (p) REVERT: e 125 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8756 (tm-30) REVERT: e 153 ARG cc_start: 0.9203 (ttp80) cc_final: 0.8920 (tmm160) REVERT: f 698 TYR cc_start: 0.8964 (t80) cc_final: 0.8656 (t80) REVERT: f 735 PHE cc_start: 0.8310 (t80) cc_final: 0.7877 (t80) outliers start: 112 outliers final: 84 residues processed: 432 average time/residue: 0.2206 time to fit residues: 156.9655 Evaluate side-chains 448 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 344 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 80 ARG Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 ASN 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 420 LEU 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 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 164 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 144 LEU 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 106 PHE 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 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 324 GLN 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 746 MET 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 910 LEU Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 184 SER Chi-restraints excluded: chain H residue 185 LEU 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 358 LYS 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 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 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 41 LEU 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 59 MET Chi-restraints excluded: chain d residue 130 CYS 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 21 GLN Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 59 MET Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain e residue 170 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 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: 8.9990 chunk 137 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 356 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 319 optimal weight: 0.0050 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 95 ASN A 128 GLN D 9 HIS d 21 GLN ** f 862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.093961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061320 restraints weight = 145118.679| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.73 r_work: 0.2826 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40216 Z= 0.127 Angle : 0.609 14.049 54875 Z= 0.311 Chirality : 0.041 0.322 6096 Planarity : 0.003 0.054 6532 Dihedral : 16.232 127.837 6453 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.60 % Allowed : 25.74 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.13), residues: 4454 helix: 2.24 (0.13), residues: 1752 sheet: 0.81 (0.19), residues: 734 loop : -0.34 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG d 161 TYR 0.022 0.001 TYR d 129 PHE 0.066 0.001 PHE E 180 TRP 0.024 0.001 TRP f 805 HIS 0.003 0.001 HIS c 89 Details of bonding type rmsd covalent geometry : bond 0.00285 (40215) covalent geometry : angle 0.60859 (54875) hydrogen bonds : bond 0.03777 ( 1968) hydrogen bonds : angle 4.22155 ( 5539) Misc. bond : bond 0.00024 ( 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 469 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 364 time to evaluate : 1.189 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: A 80 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8787 (ptt90) REVERT: A 185 ARG cc_start: 0.9212 (mmm160) cc_final: 0.8952 (mmm160) REVERT: A 421 ASP cc_start: 0.8111 (t0) cc_final: 0.7827 (t0) REVERT: A 453 MET cc_start: 0.8848 (mmm) cc_final: 0.8521 (mmm) REVERT: B 14 MET cc_start: 0.8446 (mmm) cc_final: 0.8043 (mmp) REVERT: B 436 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8508 (p) REVERT: B 452 ASN cc_start: 0.8869 (m-40) cc_final: 0.8602 (m110) REVERT: C 85 LYS cc_start: 0.8548 (pttm) cc_final: 0.8103 (mtmm) REVERT: C 195 ILE cc_start: 0.9538 (tp) cc_final: 0.9248 (pt) REVERT: D 59 MET cc_start: 0.7509 (ppp) cc_final: 0.6762 (ppp) REVERT: D 150 ARG cc_start: 0.9324 (tmm-80) cc_final: 0.9032 (tmm-80) REVERT: D 176 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9240 (pp) REVERT: D 177 TYR cc_start: 0.9076 (m-80) cc_final: 0.8501 (m-80) REVERT: E 150 ARG cc_start: 0.9020 (tmm-80) cc_final: 0.8425 (tmm-80) REVERT: F 95 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8751 (tm-30) REVERT: F 108 LYS cc_start: 0.8711 (ttpt) cc_final: 0.8119 (tptt) REVERT: F 121 ASP cc_start: 0.8449 (m-30) cc_final: 0.8192 (m-30) REVERT: F 286 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8804 (t0) REVERT: F 308 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: F 616 TYR cc_start: 0.8091 (m-80) cc_final: 0.7843 (m-80) REVERT: F 725 TRP cc_start: 0.8800 (t60) cc_final: 0.8425 (t60) REVERT: F 728 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8840 (mt-10) REVERT: F 746 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: F 778 PHE cc_start: 0.9097 (m-80) cc_final: 0.8365 (m-80) REVERT: F 910 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8594 (mt) REVERT: a 135 MET cc_start: 0.9011 (mmt) cc_final: 0.8797 (mmt) REVERT: a 199 PHE cc_start: 0.8645 (t80) cc_final: 0.8433 (t80) REVERT: a 358 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9102 (ttpt) REVERT: b 14 MET cc_start: 0.8613 (ttt) cc_final: 0.8181 (tpp) REVERT: b 20 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6136 (ptm) REVERT: b 99 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8371 (mm-40) REVERT: b 127 PHE cc_start: 0.8191 (m-80) cc_final: 0.7782 (m-80) REVERT: b 210 MET cc_start: 0.9198 (ppp) cc_final: 0.8760 (pmm) REVERT: b 215 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7343 (mm) REVERT: b 277 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8301 (p) REVERT: b 306 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8049 (tp) REVERT: c 50 ASP cc_start: 0.7570 (p0) cc_final: 0.7355 (p0) REVERT: c 167 TYR cc_start: 0.7474 (t80) cc_final: 0.7231 (t80) REVERT: d 59 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8738 (ttp) REVERT: d 61 MET cc_start: 0.7861 (ttp) cc_final: 0.6960 (tmm) REVERT: d 96 PHE cc_start: 0.8881 (p90) cc_final: 0.8356 (p90) REVERT: d 138 GLN cc_start: 0.9395 (tp40) cc_final: 0.8857 (tm-30) REVERT: d 172 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9540 (pp) REVERT: d 192 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8880 (mmm160) REVERT: e 59 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8591 (mmm) REVERT: e 89 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8321 (p) REVERT: e 125 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8685 (tm-30) REVERT: e 153 ARG cc_start: 0.9168 (ttp80) cc_final: 0.8909 (tmm160) REVERT: f 689 ILE cc_start: 0.9083 (tt) cc_final: 0.8864 (mp) REVERT: f 698 TYR cc_start: 0.8856 (t80) cc_final: 0.8536 (t80) REVERT: f 735 PHE cc_start: 0.8194 (t80) cc_final: 0.7702 (t80) outliers start: 105 outliers final: 78 residues processed: 441 average time/residue: 0.2022 time to fit residues: 147.9928 Evaluate side-chains 447 residues out of total 4030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 350 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 80 ARG Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 95 ASN 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 420 LEU 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 11 VAL Chi-restraints excluded: chain B residue 152 HIS 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 164 ILE Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 84 TYR Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 144 LEU 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 106 PHE 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 213 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain F residue 324 GLN 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 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 746 MET 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 910 LEU 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 358 LYS Chi-restraints excluded: chain a residue 497 LEU 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 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 277 THR 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 41 LEU 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 d residue 9 HIS Chi-restraints excluded: chain d residue 59 MET Chi-restraints excluded: chain d residue 130 CYS Chi-restraints excluded: chain d residue 148 ASN Chi-restraints excluded: chain d residue 172 LEU Chi-restraints excluded: chain d residue 177 TYR Chi-restraints excluded: chain e residue 21 GLN Chi-restraints excluded: chain e residue 37 THR Chi-restraints excluded: chain e residue 57 ASP Chi-restraints excluded: chain e residue 59 MET Chi-restraints excluded: chain e residue 87 ASN Chi-restraints excluded: chain e residue 89 SER Chi-restraints excluded: chain e residue 125 GLU Chi-restraints excluded: chain e residue 170 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 746 MET 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: 9.9990 chunk 439 optimal weight: 0.0870 chunk 393 optimal weight: 3.9990 chunk 269 optimal weight: 5.9990 chunk 39 optimal weight: 0.0870 chunk 336 optimal weight: 0.1980 chunk 432 optimal weight: 7.9990 chunk 337 optimal weight: 3.9990 chunk 451 optimal weight: 40.0000 chunk 171 optimal weight: 0.6980 chunk 398 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** d 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3830 r_free = 0.3830 target = 0.094512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.061749 restraints weight = 167468.907| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.98 r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40216 Z= 0.117 Angle : 0.607 13.847 54875 Z= 0.310 Chirality : 0.040 0.307 6096 Planarity : 0.003 0.054 6532 Dihedral : 16.154 126.835 6453 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.33 % Allowed : 26.02 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.13), residues: 4454 helix: 2.27 (0.13), residues: 1753 sheet: 0.81 (0.19), residues: 739 loop : -0.32 (0.14), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG d 161 TYR 0.022 0.001 TYR d 129 PHE 0.064 0.001 PHE E 180 TRP 0.024 0.001 TRP f 805 HIS 0.008 0.000 HIS c 89 Details of bonding type rmsd covalent geometry : bond 0.00256 (40215) covalent geometry : angle 0.60671 (54875) hydrogen bonds : bond 0.03651 ( 1968) hydrogen bonds : angle 4.16970 ( 5539) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18019.10 seconds wall clock time: 307 minutes 5.99 seconds (18425.99 seconds total)