Starting phenix.real_space_refine on Wed Mar 4 13:50:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqv_28547/03_2026/8eqv_28547.cif" } resolution = 3.64 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 8839 2.51 5 N 2459 2.21 5 O 2579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13974 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3117 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 22, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 870 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2902 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 12, 'TRANS': 349} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3519 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 10 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 212 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 9, 'ASP:plan': 3, 'GLU:plan': 8, 'PHE:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'GLN:plan1': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 159 Chain: "B" Number of atoms: 3566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3566 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 418} Chain breaks: 7 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 3.09, per 1000 atoms: 0.22 Number of scatterers: 13974 At special positions: 0 Unit cell: (92.88, 109.22, 170.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 2579 8.00 N 2459 7.00 C 8839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 409 " - pdb=" SG CYS E 429 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS D 523 " - pdb=" SG CYS D 547 " distance=2.04 Simple disulfide: pdb=" SG CYS D 523 " - pdb=" SG CYS D 549 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 549 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 553 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 611.6 milliseconds 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 23 sheets defined 23.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.628A pdb=" N GLY A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.330A pdb=" N TYR A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 418 removed outlier: 3.518A pdb=" N HIS C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 468 removed outlier: 3.728A pdb=" N HIS C 468 " --> pdb=" O SER C 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 465 through 468' Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 481 through 486 removed outlier: 4.200A pdb=" N LEU C 486 " --> pdb=" O LYS C 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 130 No H-bonds generated for 'chain 'E' and resid 128 through 130' Processing helix chain 'E' and resid 267 through 278 Processing helix chain 'E' and resid 281 through 285 removed outlier: 3.919A pdb=" N THR E 285 " --> pdb=" O PRO E 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 19 Processing helix chain 'D' and resid 23 through 61 removed outlier: 3.623A pdb=" N GLU D 51 " --> pdb=" O GLN D 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 52 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.578A pdb=" N SER D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.602A pdb=" N LEU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 435 through 448 removed outlier: 3.787A pdb=" N MET D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 458 Processing helix chain 'D' and resid 462 through 475 Processing helix chain 'D' and resid 571 through 576 removed outlier: 3.860A pdb=" N ALA D 576 " --> pdb=" O PRO D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 609 removed outlier: 4.276A pdb=" N ARG D 608 " --> pdb=" O CYS D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 659 Processing helix chain 'D' and resid 682 through 686 removed outlier: 3.796A pdb=" N PHE D 686 " --> pdb=" O LYS D 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 90 Processing helix chain 'B' and resid 90 through 107 removed outlier: 3.990A pdb=" N GLN B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 removed outlier: 3.575A pdb=" N LEU B 115 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR B 116 " --> pdb=" O ARG B 113 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR B 117 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET B 118 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 119 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS B 120 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.669A pdb=" N MET B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 471 removed outlier: 3.512A pdb=" N HIS B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 601 Processing helix chain 'B' and resid 607 through 625 removed outlier: 4.613A pdb=" N VAL B 613 " --> pdb=" O GLY B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 643 removed outlier: 4.601A pdb=" N HIS B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 651 Processing helix chain 'B' and resid 652 through 666 Processing helix chain 'B' and resid 670 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.522A pdb=" N LEU A 34 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP A 379 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 4.109A pdb=" N ASN A 77 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 121 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 83 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE A 117 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N GLN A 85 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 115 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 132 removed outlier: 3.613A pdb=" N ARG A 131 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 141 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 140 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 151 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.677A pdb=" N GLY A 182 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 221 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 235 removed outlier: 4.135A pdb=" N PHE A 243 " --> pdb=" O TRP A 255 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A 247 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS A 267 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 281 removed outlier: 6.734A pdb=" N GLY A 292 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 279 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 290 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N PHE A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE A 288 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 289 " --> pdb=" O TRP A 301 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 291 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 325 removed outlier: 3.547A pdb=" N GLN A 322 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 427 through 431 Processing sheet with id=AA9, first strand: chain 'C' and resid 461 through 463 removed outlier: 4.450A pdb=" N ALA C 436 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE C 435 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 318 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 354 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE B 164 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN B 356 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 413 through 418 removed outlier: 4.745A pdb=" N GLN E 415 " --> pdb=" O VAL E 428 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 428 " --> pdb=" O GLN E 415 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA E 427 " --> pdb=" O TRP E 435 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER E 433 " --> pdb=" O CYS E 429 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG E 436 " --> pdb=" O ASN E 86 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASN E 86 " --> pdb=" O ARG E 436 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP E 438 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N CYS E 84 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 89 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 98 through 101 removed outlier: 3.728A pdb=" N GLY E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 116 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL E 121 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER E 137 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 123 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N LYS D 99 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER E 137 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 154 removed outlier: 7.090A pdb=" N ALA E 166 " --> pdb=" O TYR E 148 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS E 150 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA E 164 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TRP E 152 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU E 162 " --> pdb=" O TRP E 152 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY E 167 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASN E 176 " --> pdb=" O CYS E 182 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N CYS E 182 " --> pdb=" O ASN E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 193 through 198 removed outlier: 3.677A pdb=" N GLU E 195 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU E 215 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE E 228 " --> pdb=" O LEU E 215 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU E 217 " --> pdb=" O VAL E 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 244 removed outlier: 3.830A pdb=" N PHE E 299 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 309 through 315 removed outlier: 4.577A pdb=" N CYS E 311 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER E 323 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS E 332 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE E 352 " --> pdb=" O LYS E 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 368 through 370 Processing sheet with id=AB8, first strand: chain 'D' and resid 114 through 115 removed outlier: 5.872A pdb=" N SER D 114 " --> pdb=" O GLY D 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 120 through 121 removed outlier: 6.474A pdb=" N PHE D 120 " --> pdb=" O ILE D 645 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 614 through 618 Processing sheet with id=AC2, first strand: chain 'D' and resid 637 through 640 removed outlier: 7.004A pdb=" N PHE D 637 " --> pdb=" O ALA D 712 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 712 " --> pdb=" O PHE D 637 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 639 " --> pdb=" O ILE D 710 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 203 through 207 removed outlier: 6.736A pdb=" N VAL B 191 " --> pdb=" O LYS B 246 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 203 through 207 removed outlier: 3.670A pdb=" N LEU B 187 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 437 through 441 removed outlier: 7.150A pdb=" N PHE B 432 " --> pdb=" O ARG B 439 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLN B 441 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR B 430 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 489 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 486 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 479 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 477 " --> pdb=" O ASP B 488 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.39 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4617 1.35 - 1.47: 3402 1.47 - 1.59: 6151 1.59 - 1.71: 0 1.71 - 1.83: 136 Bond restraints: 14306 Sorted by residual: bond pdb=" CA ASP E 212 " pdb=" C ASP E 212 " ideal model delta sigma weight residual 1.523 1.495 0.029 1.56e-02 4.11e+03 3.37e+00 bond pdb=" C LYS A 143 " pdb=" N THR A 144 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.24e+00 bond pdb=" C MET C 452 " pdb=" N PRO C 453 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.89e+00 bond pdb=" CA ASN B 216 " pdb=" CB ASN B 216 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.53e+00 bond pdb=" CA ASP E 395 " pdb=" C ASP E 395 " ideal model delta sigma weight residual 1.524 1.539 -0.015 1.26e-02 6.30e+03 1.49e+00 ... (remaining 14301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 19148 2.82 - 5.65: 214 5.65 - 8.47: 13 8.47 - 11.29: 2 11.29 - 14.11: 1 Bond angle restraints: 19378 Sorted by residual: angle pdb=" C LYS A 143 " pdb=" N THR A 144 " pdb=" CA THR A 144 " ideal model delta sigma weight residual 120.68 134.79 -14.11 1.52e+00 4.33e-01 8.62e+01 angle pdb=" C ARG B 253 " pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 121.97 131.15 -9.18 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C LYS B 537 " pdb=" CA LYS B 537 " pdb=" CB LYS B 537 " ideal model delta sigma weight residual 115.79 110.16 5.63 1.19e+00 7.06e-01 2.23e+01 angle pdb=" N VAL D 691 " pdb=" CA VAL D 691 " pdb=" C VAL D 691 " ideal model delta sigma weight residual 111.90 108.70 3.20 8.10e-01 1.52e+00 1.57e+01 angle pdb=" N ILE D 538 " pdb=" CA ILE D 538 " pdb=" C ILE D 538 " ideal model delta sigma weight residual 112.80 108.52 4.28 1.15e+00 7.56e-01 1.38e+01 ... (remaining 19373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 7437 17.81 - 35.61: 912 35.61 - 53.42: 197 53.42 - 71.23: 30 71.23 - 89.03: 16 Dihedral angle restraints: 8592 sinusoidal: 3418 harmonic: 5174 Sorted by residual: dihedral pdb=" CB CYS D 523 " pdb=" SG CYS D 523 " pdb=" SG CYS D 549 " pdb=" CB CYS D 549 " ideal model delta sinusoidal sigma weight residual -86.00 -144.69 58.69 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CA ASP D 531 " pdb=" C ASP D 531 " pdb=" N SER D 532 " pdb=" CA SER D 532 " ideal model delta harmonic sigma weight residual -180.00 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA CYS D 294 " pdb=" C CYS D 294 " pdb=" N PHE D 295 " pdb=" CA PHE D 295 " ideal model delta harmonic sigma weight residual 180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 8589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1443 0.037 - 0.074: 472 0.074 - 0.111: 164 0.111 - 0.148: 39 0.148 - 0.185: 3 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA ASP E 395 " pdb=" N ASP E 395 " pdb=" C ASP E 395 " pdb=" CB ASP E 395 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA GLU C 454 " pdb=" N GLU C 454 " pdb=" C GLU C 454 " pdb=" CB GLU C 454 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" CB ILE A 369 " pdb=" CA ILE A 369 " pdb=" CG1 ILE A 369 " pdb=" CG2 ILE A 369 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 2118 not shown) Planarity restraints: 2499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 96 " 0.048 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO D 97 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 97 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 97 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 32 " -0.015 2.00e-02 2.50e+03 1.60e-02 4.50e+00 pdb=" CG PHE D 32 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE D 32 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 32 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 32 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 32 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 253 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C ARG B 253 " -0.036 2.00e-02 2.50e+03 pdb=" O ARG B 253 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 254 " 0.012 2.00e-02 2.50e+03 ... (remaining 2496 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 947 2.73 - 3.27: 13920 3.27 - 3.82: 22540 3.82 - 4.36: 26390 4.36 - 4.90: 45043 Nonbonded interactions: 108840 Sorted by model distance: nonbonded pdb=" OD1 ASP D 676 " pdb=" OG1 THR D 678 " model vdw 2.188 3.040 nonbonded pdb=" O LEU B 311 " pdb=" OH TYR B 315 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" O PRO A 327 " model vdw 2.226 3.040 nonbonded pdb=" OE2 GLU A 13 " pdb=" NH2 ARG B 103 " model vdw 2.227 3.120 nonbonded pdb=" O HIS D 593 " pdb=" NH2 ARG D 608 " model vdw 2.235 3.120 ... (remaining 108835 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.06 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.290 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.039 14312 Z= 0.171 Angle : 0.783 14.114 19390 Z= 0.472 Chirality : 0.043 0.185 2121 Planarity : 0.005 0.074 2499 Dihedral : 16.230 89.034 5192 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.26 % Favored : 91.51 % Rotamer: Outliers : 0.13 % Allowed : 21.16 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.20), residues: 1719 helix: 0.89 (0.29), residues: 343 sheet: -1.38 (0.26), residues: 393 loop : -2.17 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 685 TYR 0.016 0.001 TYR A 284 PHE 0.037 0.002 PHE D 32 TRP 0.027 0.002 TRP B 361 HIS 0.010 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00321 (14306) covalent geometry : angle 0.78200 (19378) SS BOND : bond 0.00681 ( 6) SS BOND : angle 1.77627 ( 12) hydrogen bonds : bond 0.17741 ( 443) hydrogen bonds : angle 7.01211 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 MET cc_start: 0.9145 (ttp) cc_final: 0.8675 (tmm) REVERT: B 243 HIS cc_start: 0.8453 (p-80) cc_final: 0.8048 (p-80) REVERT: B 244 MET cc_start: 0.8190 (mmt) cc_final: 0.7871 (mtp) REVERT: B 299 MET cc_start: 0.9488 (ttm) cc_final: 0.8983 (tpp) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.1128 time to fit residues: 18.1929 Evaluate side-chains 72 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 261 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 HIS A 316 HIS ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 456 ASN ** B 624 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 = 0.3275 r_free = 0.3275 target = 0.049903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036676 restraints weight = 83496.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037898 restraints weight = 41435.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.038672 restraints weight = 27369.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039163 restraints weight = 21135.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039508 restraints weight = 18114.938| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14312 Z= 0.230 Angle : 0.672 9.404 19390 Z= 0.352 Chirality : 0.044 0.211 2121 Planarity : 0.005 0.070 2499 Dihedral : 4.947 27.749 1880 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 3.31 % Allowed : 18.92 % Favored : 77.78 % 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 are not related in a simple way. whole: -1.66 (0.20), residues: 1719 helix: 1.03 (0.28), residues: 363 sheet: -1.05 (0.26), residues: 411 loop : -2.06 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 287 TYR 0.023 0.002 TYR E 80 PHE 0.025 0.002 PHE D 32 TRP 0.013 0.002 TRP B 361 HIS 0.010 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00510 (14306) covalent geometry : angle 0.67077 (19378) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.47419 ( 12) hydrogen bonds : bond 0.04762 ( 443) hydrogen bonds : angle 5.38655 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 72 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.6969 (p0) REVERT: A 253 MET cc_start: 0.7970 (ttp) cc_final: 0.7541 (mtm) REVERT: A 342 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9232 (tt) REVERT: C 454 GLU cc_start: 0.8283 (pp20) cc_final: 0.8002 (pp20) REVERT: E 252 MET cc_start: 0.8775 (tpt) cc_final: 0.8456 (tpt) REVERT: D 263 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8469 (m-40) REVERT: D 439 MET cc_start: 0.9531 (ttp) cc_final: 0.8812 (tmm) REVERT: B 243 HIS cc_start: 0.8389 (p-80) cc_final: 0.8066 (p-80) REVERT: B 244 MET cc_start: 0.8239 (mmt) cc_final: 0.7915 (mtp) REVERT: B 299 MET cc_start: 0.9364 (ttm) cc_final: 0.9023 (tpp) outliers start: 50 outliers final: 19 residues processed: 116 average time/residue: 0.0856 time to fit residues: 16.5899 Evaluate side-chains 90 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 446 ASP Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 614 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 90 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS D 45 ASN ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 624 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 = 0.3281 r_free = 0.3281 target = 0.050169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036854 restraints weight = 83311.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038088 restraints weight = 41146.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.038867 restraints weight = 27140.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.039394 restraints weight = 20976.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.039692 restraints weight = 17767.158| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14312 Z= 0.131 Angle : 0.575 8.183 19390 Z= 0.302 Chirality : 0.043 0.198 2121 Planarity : 0.004 0.063 2499 Dihedral : 4.643 25.388 1880 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.17 % Favored : 93.60 % Rotamer: Outliers : 2.78 % Allowed : 19.71 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.20), residues: 1719 helix: 1.38 (0.28), residues: 363 sheet: -0.79 (0.26), residues: 412 loop : -1.92 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 456 TYR 0.010 0.001 TYR E 244 PHE 0.021 0.001 PHE D 32 TRP 0.016 0.001 TRP B 361 HIS 0.006 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00291 (14306) covalent geometry : angle 0.57419 (19378) SS BOND : bond 0.00447 ( 6) SS BOND : angle 1.27975 ( 12) hydrogen bonds : bond 0.04193 ( 443) hydrogen bonds : angle 4.88153 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 MET cc_start: 0.8092 (ttp) cc_final: 0.7622 (mtm) REVERT: A 342 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9223 (tt) REVERT: C 454 GLU cc_start: 0.8385 (pp20) cc_final: 0.8044 (pp20) REVERT: E 252 MET cc_start: 0.8683 (tpt) cc_final: 0.8352 (tpt) REVERT: D 439 MET cc_start: 0.9570 (ttp) cc_final: 0.8833 (tmm) REVERT: B 243 HIS cc_start: 0.8229 (p90) cc_final: 0.8011 (p-80) REVERT: B 244 MET cc_start: 0.8206 (mmt) cc_final: 0.7896 (mtp) REVERT: B 299 MET cc_start: 0.9387 (ttm) cc_final: 0.8994 (tpp) outliers start: 42 outliers final: 18 residues processed: 105 average time/residue: 0.0853 time to fit residues: 14.9784 Evaluate side-chains 85 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 145 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN E 104 HIS ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 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 = 0.3247 r_free = 0.3247 target = 0.048461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.035165 restraints weight = 86270.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.036195 restraints weight = 47331.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036884 restraints weight = 33083.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037300 restraints weight = 26506.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037599 restraints weight = 23228.592| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14312 Z= 0.319 Angle : 0.708 9.569 19390 Z= 0.368 Chirality : 0.046 0.223 2121 Planarity : 0.005 0.059 2499 Dihedral : 4.978 25.677 1880 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.78 % Favored : 90.98 % Rotamer: Outliers : 4.03 % Allowed : 19.31 % Favored : 76.65 % 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 are not related in a simple way. whole: -1.47 (0.20), residues: 1719 helix: 1.17 (0.28), residues: 363 sheet: -0.89 (0.26), residues: 410 loop : -1.95 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 427 TYR 0.022 0.002 TYR E 244 PHE 0.016 0.002 PHE B 666 TRP 0.009 0.001 TRP B 361 HIS 0.010 0.002 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00708 (14306) covalent geometry : angle 0.70755 (19378) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.59141 ( 12) hydrogen bonds : bond 0.04918 ( 443) hydrogen bonds : angle 5.16036 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 63 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7710 (p0) REVERT: A 253 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8171 (mtm) REVERT: A 342 LEU cc_start: 0.9552 (OUTLIER) cc_final: 0.9334 (tt) REVERT: C 398 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.8321 (t80) REVERT: C 454 GLU cc_start: 0.8320 (pp20) cc_final: 0.7908 (pp20) REVERT: E 308 TYR cc_start: 0.6931 (m-10) cc_final: 0.6697 (m-10) REVERT: D 110 MET cc_start: 0.9146 (ttt) cc_final: 0.8560 (ttt) REVERT: D 439 MET cc_start: 0.9335 (ttp) cc_final: 0.8675 (tmm) REVERT: D 701 MET cc_start: 0.8800 (tpp) cc_final: 0.8416 (tpp) REVERT: B 156 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8935 (m-70) REVERT: B 243 HIS cc_start: 0.8390 (p90) cc_final: 0.8008 (p-80) REVERT: B 244 MET cc_start: 0.8158 (mmt) cc_final: 0.7536 (tpt) REVERT: B 299 MET cc_start: 0.9409 (ttm) cc_final: 0.8965 (tpp) REVERT: B 672 MET cc_start: 0.8817 (mmm) cc_final: 0.8591 (tmm) outliers start: 61 outliers final: 30 residues processed: 115 average time/residue: 0.0906 time to fit residues: 17.1616 Evaluate side-chains 95 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 245 ASP Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 695 CYS Chi-restraints excluded: chain D residue 724 PHE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 85 optimal weight: 40.0000 chunk 139 optimal weight: 9.9990 chunk 157 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.049125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.035700 restraints weight = 84487.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036786 restraints weight = 45367.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.037510 restraints weight = 31443.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.037917 restraints weight = 25007.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038234 restraints weight = 21903.969| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14312 Z= 0.177 Angle : 0.596 9.424 19390 Z= 0.311 Chirality : 0.043 0.186 2121 Planarity : 0.004 0.057 2499 Dihedral : 4.749 22.591 1880 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.63 % Favored : 93.14 % Rotamer: Outliers : 3.11 % Allowed : 20.50 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1719 helix: 1.40 (0.28), residues: 364 sheet: -0.69 (0.26), residues: 410 loop : -1.86 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 456 TYR 0.011 0.001 TYR E 244 PHE 0.014 0.001 PHE D 32 TRP 0.013 0.001 TRP B 361 HIS 0.008 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00398 (14306) covalent geometry : angle 0.59536 (19378) SS BOND : bond 0.00301 ( 6) SS BOND : angle 1.31086 ( 12) hydrogen bonds : bond 0.04238 ( 443) hydrogen bonds : angle 4.83307 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 62 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7751 (p0) REVERT: A 253 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8064 (mtm) REVERT: A 342 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9308 (tt) REVERT: C 398 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8299 (t80) REVERT: C 454 GLU cc_start: 0.8347 (pp20) cc_final: 0.7910 (pp20) REVERT: E 252 MET cc_start: 0.8842 (tpt) cc_final: 0.8588 (tpt) REVERT: D 110 MET cc_start: 0.9213 (ttt) cc_final: 0.8591 (ttt) REVERT: D 439 MET cc_start: 0.9401 (ttp) cc_final: 0.8713 (tmm) REVERT: D 701 MET cc_start: 0.8829 (tpp) cc_final: 0.8466 (tpp) REVERT: B 156 HIS cc_start: 0.9150 (OUTLIER) cc_final: 0.8908 (m-70) REVERT: B 243 HIS cc_start: 0.8332 (p90) cc_final: 0.8003 (p-80) REVERT: B 244 MET cc_start: 0.8241 (mmt) cc_final: 0.7886 (mtp) REVERT: B 299 MET cc_start: 0.9407 (ttm) cc_final: 0.8958 (tpp) REVERT: B 663 MET cc_start: 0.9437 (tpp) cc_final: 0.9231 (tpp) REVERT: B 672 MET cc_start: 0.8794 (mmm) cc_final: 0.8454 (tmm) outliers start: 47 outliers final: 29 residues processed: 100 average time/residue: 0.0935 time to fit residues: 15.4192 Evaluate side-chains 96 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 302 ARG Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 76 optimal weight: 0.0270 chunk 116 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 297 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 624 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 = 0.3253 r_free = 0.3253 target = 0.049044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.035742 restraints weight = 83002.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036929 restraints weight = 41081.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037673 restraints weight = 27156.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038181 restraints weight = 21065.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038459 restraints weight = 17922.084| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14312 Z= 0.111 Angle : 0.564 10.719 19390 Z= 0.291 Chirality : 0.043 0.177 2121 Planarity : 0.004 0.057 2499 Dihedral : 4.506 20.353 1880 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.04 % Favored : 92.79 % Rotamer: Outliers : 2.45 % Allowed : 21.10 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.20), residues: 1719 helix: 1.50 (0.28), residues: 366 sheet: -0.43 (0.27), residues: 400 loop : -1.71 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 456 TYR 0.011 0.001 TYR E 244 PHE 0.014 0.001 PHE A 243 TRP 0.014 0.001 TRP B 361 HIS 0.008 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00247 (14306) covalent geometry : angle 0.56337 (19378) SS BOND : bond 0.00372 ( 6) SS BOND : angle 1.18971 ( 12) hydrogen bonds : bond 0.03667 ( 443) hydrogen bonds : angle 4.53005 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 66 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7612 (p0) REVERT: A 253 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7817 (mtm) REVERT: A 342 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9186 (tt) REVERT: C 454 GLU cc_start: 0.8481 (pp20) cc_final: 0.8092 (pp20) REVERT: E 252 MET cc_start: 0.8750 (tpt) cc_final: 0.8420 (tpt) REVERT: D 41 MET cc_start: 0.9445 (ttt) cc_final: 0.9131 (ttm) REVERT: D 110 MET cc_start: 0.9345 (ttt) cc_final: 0.8688 (ttt) REVERT: D 439 MET cc_start: 0.9580 (ttp) cc_final: 0.8828 (ppp) REVERT: D 701 MET cc_start: 0.8484 (tpp) cc_final: 0.8084 (tpp) REVERT: B 156 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8971 (m-70) REVERT: B 243 HIS cc_start: 0.8212 (p90) cc_final: 0.7978 (p-80) REVERT: B 244 MET cc_start: 0.8252 (mmt) cc_final: 0.7928 (mtp) REVERT: B 299 MET cc_start: 0.9339 (ttm) cc_final: 0.8934 (tpp) REVERT: B 672 MET cc_start: 0.9013 (mmm) cc_final: 0.8461 (tmm) outliers start: 37 outliers final: 23 residues processed: 94 average time/residue: 0.0954 time to fit residues: 14.7016 Evaluate side-chains 89 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 302 ARG Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 109 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.047697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.034507 restraints weight = 87074.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035517 restraints weight = 47100.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036199 restraints weight = 32820.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.036635 restraints weight = 26294.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.036846 restraints weight = 22901.267| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 14312 Z= 0.343 Angle : 0.732 11.675 19390 Z= 0.376 Chirality : 0.045 0.177 2121 Planarity : 0.005 0.057 2499 Dihedral : 5.002 27.502 1880 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.42 % Favored : 90.40 % Rotamer: Outliers : 3.04 % Allowed : 20.90 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.20), residues: 1719 helix: 1.26 (0.28), residues: 364 sheet: -0.65 (0.26), residues: 405 loop : -1.86 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 439 TYR 0.020 0.002 TYR E 244 PHE 0.015 0.002 PHE E 82 TRP 0.010 0.002 TRP A 42 HIS 0.007 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00765 (14306) covalent geometry : angle 0.73085 (19378) SS BOND : bond 0.00394 ( 6) SS BOND : angle 1.86305 ( 12) hydrogen bonds : bond 0.04840 ( 443) hydrogen bonds : angle 5.06768 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 57 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7869 (p0) REVERT: A 253 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8148 (mtm) REVERT: A 342 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9303 (tt) REVERT: C 398 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8349 (t80) REVERT: C 454 GLU cc_start: 0.8331 (pp20) cc_final: 0.7920 (pp20) REVERT: D 121 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8610 (ttm) REVERT: D 439 MET cc_start: 0.9282 (ttp) cc_final: 0.8660 (ppp) REVERT: D 701 MET cc_start: 0.8856 (tpp) cc_final: 0.8648 (tpp) REVERT: B 244 MET cc_start: 0.8283 (mmt) cc_final: 0.7620 (mmm) REVERT: B 299 MET cc_start: 0.9374 (ttm) cc_final: 0.8854 (tpp) REVERT: B 672 MET cc_start: 0.8831 (mmm) cc_final: 0.8495 (tmm) outliers start: 46 outliers final: 26 residues processed: 92 average time/residue: 0.0974 time to fit residues: 14.7222 Evaluate side-chains 87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 56 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain D residue 724 PHE Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 614 MET Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 125 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** B 624 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 = 0.3270 r_free = 0.3270 target = 0.048974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035641 restraints weight = 84233.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036738 restraints weight = 44535.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037442 restraints weight = 30463.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037914 restraints weight = 24291.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.038187 restraints weight = 20962.292| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14312 Z= 0.131 Angle : 0.586 12.323 19390 Z= 0.299 Chirality : 0.043 0.181 2121 Planarity : 0.004 0.062 2499 Dihedral : 4.643 23.130 1880 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.81 % Favored : 93.02 % Rotamer: Outliers : 2.05 % Allowed : 21.89 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.21), residues: 1719 helix: 1.44 (0.28), residues: 368 sheet: -0.43 (0.27), residues: 410 loop : -1.69 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.009 0.001 TYR D 518 PHE 0.014 0.001 PHE A 243 TRP 0.013 0.001 TRP B 361 HIS 0.006 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00298 (14306) covalent geometry : angle 0.58482 (19378) SS BOND : bond 0.00325 ( 6) SS BOND : angle 1.34864 ( 12) hydrogen bonds : bond 0.03882 ( 443) hydrogen bonds : angle 4.61568 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7815 (p0) REVERT: A 253 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: A 342 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9283 (tt) REVERT: C 398 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8303 (t80) REVERT: C 454 GLU cc_start: 0.8357 (pp20) cc_final: 0.7941 (pp20) REVERT: D 110 MET cc_start: 0.9182 (ttt) cc_final: 0.8576 (ttt) REVERT: D 439 MET cc_start: 0.9387 (ttp) cc_final: 0.8713 (ppp) REVERT: D 701 MET cc_start: 0.8722 (tpp) cc_final: 0.8458 (tpp) REVERT: B 244 MET cc_start: 0.8252 (mmt) cc_final: 0.7593 (mmm) REVERT: B 299 MET cc_start: 0.9369 (ttm) cc_final: 0.8821 (tpp) REVERT: B 672 MET cc_start: 0.8897 (mmm) cc_final: 0.8472 (tmm) outliers start: 31 outliers final: 22 residues processed: 84 average time/residue: 0.0867 time to fit residues: 12.2394 Evaluate side-chains 86 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 398 PHE Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 484 THR Chi-restraints excluded: chain E residue 237 ASP Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 9 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 129 optimal weight: 0.4980 chunk 123 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.048851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.035566 restraints weight = 84432.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.036731 restraints weight = 41900.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037476 restraints weight = 27762.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037987 restraints weight = 21545.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.038292 restraints weight = 18303.792| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14312 Z= 0.102 Angle : 0.563 12.702 19390 Z= 0.285 Chirality : 0.042 0.185 2121 Planarity : 0.004 0.061 2499 Dihedral : 4.351 20.167 1880 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.46 % Favored : 93.37 % Rotamer: Outliers : 1.79 % Allowed : 22.22 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.21), residues: 1719 helix: 1.61 (0.28), residues: 362 sheet: -0.26 (0.27), residues: 396 loop : -1.57 (0.19), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 682 TYR 0.011 0.001 TYR B 315 PHE 0.016 0.001 PHE D 451 TRP 0.013 0.001 TRP B 361 HIS 0.007 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00230 (14306) covalent geometry : angle 0.56190 (19378) SS BOND : bond 0.00409 ( 6) SS BOND : angle 1.20791 ( 12) hydrogen bonds : bond 0.03376 ( 443) hydrogen bonds : angle 4.37046 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7638 (p0) REVERT: A 253 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7795 (mtm) REVERT: A 342 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9204 (tt) REVERT: C 454 GLU cc_start: 0.8501 (pp20) cc_final: 0.8095 (pp20) REVERT: E 180 MET cc_start: 0.9019 (mtt) cc_final: 0.8796 (mtp) REVERT: D 110 MET cc_start: 0.9342 (ttt) cc_final: 0.8749 (ttt) REVERT: D 439 MET cc_start: 0.9547 (ttp) cc_final: 0.8804 (ppp) REVERT: B 299 MET cc_start: 0.9290 (ttm) cc_final: 0.8844 (tpp) REVERT: B 672 MET cc_start: 0.9068 (mmm) cc_final: 0.8466 (tmm) outliers start: 27 outliers final: 19 residues processed: 81 average time/residue: 0.0914 time to fit residues: 12.4559 Evaluate side-chains 83 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 161 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.0170 chunk 72 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 431 HIS ** D 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 624 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 = 0.3245 r_free = 0.3245 target = 0.048670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.035386 restraints weight = 84888.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.036557 restraints weight = 42047.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.037319 restraints weight = 27709.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.037827 restraints weight = 21478.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038103 restraints weight = 18262.385| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14312 Z= 0.111 Angle : 0.575 13.150 19390 Z= 0.286 Chirality : 0.042 0.182 2121 Planarity : 0.004 0.059 2499 Dihedral : 4.259 20.820 1880 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % Rotamer: Outliers : 1.79 % Allowed : 22.29 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.21), residues: 1719 helix: 1.67 (0.28), residues: 363 sheet: -0.18 (0.27), residues: 399 loop : -1.50 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.008 0.001 TYR E 244 PHE 0.012 0.001 PHE A 243 TRP 0.013 0.001 TRP B 361 HIS 0.006 0.001 HIS D 706 Details of bonding type rmsd covalent geometry : bond 0.00254 (14306) covalent geometry : angle 0.57430 (19378) SS BOND : bond 0.00376 ( 6) SS BOND : angle 1.20978 ( 12) hydrogen bonds : bond 0.03332 ( 443) hydrogen bonds : angle 4.28982 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3438 Ramachandran restraints generated. 1719 Oldfield, 0 Emsley, 1719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7603 (p0) REVERT: A 253 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7787 (mtm) REVERT: A 342 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9232 (tt) REVERT: C 454 GLU cc_start: 0.8489 (pp20) cc_final: 0.8102 (pp20) REVERT: E 180 MET cc_start: 0.9066 (mtt) cc_final: 0.8820 (mtp) REVERT: D 110 MET cc_start: 0.9329 (ttt) cc_final: 0.8735 (ttt) REVERT: D 439 MET cc_start: 0.9557 (ttp) cc_final: 0.8816 (ppp) REVERT: D 701 MET cc_start: 0.8577 (tpp) cc_final: 0.8166 (mmm) REVERT: B 244 MET cc_start: 0.8381 (mmt) cc_final: 0.7943 (mmm) REVERT: B 299 MET cc_start: 0.9317 (ttm) cc_final: 0.8874 (tpp) REVERT: B 672 MET cc_start: 0.9071 (mmm) cc_final: 0.8470 (tmm) outliers start: 27 outliers final: 20 residues processed: 82 average time/residue: 0.0904 time to fit residues: 12.4197 Evaluate side-chains 85 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 62 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 253 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 271 MET Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 547 CYS Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 657 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 160 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 139 optimal weight: 0.0770 chunk 123 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 HIS ** B 624 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 = 0.3252 r_free = 0.3252 target = 0.048931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035696 restraints weight = 83410.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036873 restraints weight = 41160.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037659 restraints weight = 27062.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038132 restraints weight = 20858.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.038482 restraints weight = 17848.057| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14312 Z= 0.095 Angle : 0.558 13.083 19390 Z= 0.280 Chirality : 0.042 0.183 2121 Planarity : 0.004 0.059 2499 Dihedral : 4.199 19.985 1880 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.88 % Favored : 93.95 % Rotamer: Outliers : 1.65 % Allowed : 22.35 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.21), residues: 1719 helix: 1.72 (0.28), residues: 363 sheet: -0.11 (0.27), residues: 394 loop : -1.47 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 682 TYR 0.009 0.001 TYR E 308 PHE 0.042 0.001 PHE D 451 TRP 0.014 0.001 TRP B 361 HIS 0.006 0.001 HIS D 706 Details of bonding type rmsd covalent geometry : bond 0.00212 (14306) covalent geometry : angle 0.55759 (19378) SS BOND : bond 0.00396 ( 6) SS BOND : angle 1.18562 ( 12) hydrogen bonds : bond 0.03210 ( 443) hydrogen bonds : angle 4.22891 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.94 seconds wall clock time: 40 minutes 4.37 seconds (2404.37 seconds total)