Starting phenix.real_space_refine on Thu Jun 12 16:01:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eqv_28547/06_2025/8eqv_28547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eqv_28547/06_2025/8eqv_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_28547/06_2025/8eqv_28547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eqv_28547/06_2025/8eqv_28547.map" model { file = "/net/cci-nas-00/data/ceres_data/8eqv_28547/06_2025/8eqv_28547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eqv_28547/06_2025/8eqv_28547.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 9} 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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 8.64, per 1000 atoms: 0.62 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: 2.94 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.80 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: 4.57 Time building geometry restraints manager: 3.58 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: 0.010 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.900 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (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 TRP 0.027 0.002 TRP B 361 HIS 0.010 0.001 HIS B 449 PHE 0.037 0.002 PHE D 32 TYR 0.016 0.001 TYR A 284 ARG 0.007 0.001 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.17741 ( 443) hydrogen bonds : angle 7.01211 ( 1260) SS BOND : bond 0.00681 ( 6) SS BOND : angle 1.77627 ( 12) covalent geometry : bond 0.00321 (14306) covalent geometry : angle 0.78200 (19378) *********************** 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 : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 439 MET cc_start: 0.9145 (ttp) cc_final: 0.8674 (tmm) REVERT: B 299 MET cc_start: 0.9488 (ttm) cc_final: 0.8982 (tpp) outliers start: 2 outliers final: 1 residues processed: 106 average time/residue: 0.2814 time to fit residues: 45.0332 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 : 1.791 ------------------------------------------------------------------------------- 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 146 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 E 397 HIS ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 297 HIS B 156 HIS B 243 HIS B 624 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.052080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038966 restraints weight = 81378.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.040266 restraints weight = 39986.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.041097 restraints weight = 26062.229| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1372 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= 0.132 Angle : 0.610 7.552 19390 Z= 0.320 Chirality : 0.043 0.201 2121 Planarity : 0.004 0.072 2499 Dihedral : 4.751 27.882 1880 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.81 % Favored : 92.96 % Rotamer: Outliers : 2.84 % Allowed : 19.18 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1719 helix: 1.18 (0.28), residues: 356 sheet: -0.92 (0.26), residues: 409 loop : -2.01 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 364 HIS 0.006 0.001 HIS D 297 PHE 0.026 0.001 PHE D 32 TYR 0.019 0.001 TYR B 434 ARG 0.004 0.000 ARG E 287 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 443) hydrogen bonds : angle 5.35342 ( 1260) SS BOND : bond 0.00459 ( 6) SS BOND : angle 1.47214 ( 12) covalent geometry : bond 0.00286 (14306) covalent geometry : angle 0.60952 (19378) *********************** 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 116 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6886 (p0) REVERT: A 253 MET cc_start: 0.7627 (ttp) cc_final: 0.7262 (mtm) REVERT: A 342 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9151 (tt) REVERT: E 308 TYR cc_start: 0.7322 (m-10) cc_final: 0.7109 (m-10) REVERT: D 439 MET cc_start: 0.9560 (ttp) cc_final: 0.8832 (tmm) REVERT: B 244 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7885 (mtp) REVERT: B 299 MET cc_start: 0.9382 (ttm) cc_final: 0.9034 (tpp) outliers start: 43 outliers final: 16 residues processed: 110 average time/residue: 0.2041 time to fit residues: 37.8098 Evaluate side-chains 87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 2.031 ------------------------------------------------------------------------------- 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 342 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 484 THR 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 635 ASN Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 481 HIS Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 596 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 75 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 146 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN B 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.051259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.038080 restraints weight = 82192.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.039352 restraints weight = 40823.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.040164 restraints weight = 26799.490| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14312 Z= 0.138 Angle : 0.574 8.693 19390 Z= 0.301 Chirality : 0.043 0.199 2121 Planarity : 0.004 0.063 2499 Dihedral : 4.569 24.889 1880 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.90 % Rotamer: Outliers : 3.24 % Allowed : 18.45 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.20), residues: 1719 helix: 1.32 (0.28), residues: 358 sheet: -0.79 (0.26), residues: 405 loop : -1.90 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 361 HIS 0.020 0.001 HIS B 243 PHE 0.022 0.001 PHE D 32 TYR 0.009 0.001 TYR C 493 ARG 0.004 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 443) hydrogen bonds : angle 4.99013 ( 1260) SS BOND : bond 0.00408 ( 6) SS BOND : angle 1.24031 ( 12) covalent geometry : bond 0.00305 (14306) covalent geometry : angle 0.57353 (19378) *********************** 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 118 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 69 time to evaluate : 1.770 Fit side-chains REVERT: A 253 MET cc_start: 0.7795 (ttp) cc_final: 0.7398 (mtm) REVERT: A 342 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9194 (tt) REVERT: C 438 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8088 (ptm160) REVERT: C 454 GLU cc_start: 0.8367 (pp20) cc_final: 0.8088 (pp20) REVERT: E 252 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8487 (tpt) REVERT: D 110 MET cc_start: 0.9156 (ttt) cc_final: 0.8797 (ttt) REVERT: D 439 MET cc_start: 0.9556 (ttp) cc_final: 0.8849 (tmm) REVERT: B 244 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7842 (mtp) REVERT: B 299 MET cc_start: 0.9396 (ttm) cc_final: 0.9057 (tpp) outliers start: 49 outliers final: 20 residues processed: 110 average time/residue: 0.2080 time to fit residues: 37.2259 Evaluate side-chains 88 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 419 ILE 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 252 MET Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 395 ASP Chi-restraints excluded: chain E residue 404 LEU 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 594 TRP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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 53 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 57 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 HIS ** B 655 ASN ** 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 = 0.3308 r_free = 0.3308 target = 0.051047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.037887 restraints weight = 81396.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039129 restraints weight = 40316.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.039916 restraints weight = 26650.045| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2240 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= 0.116 Angle : 0.562 8.842 19390 Z= 0.290 Chirality : 0.043 0.185 2121 Planarity : 0.004 0.061 2499 Dihedral : 4.392 21.647 1880 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.34 % Favored : 93.43 % Rotamer: Outliers : 2.78 % Allowed : 19.11 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1719 helix: 1.45 (0.28), residues: 360 sheet: -0.54 (0.26), residues: 399 loop : -1.76 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 361 HIS 0.005 0.001 HIS A 176 PHE 0.018 0.001 PHE D 32 TYR 0.010 0.001 TYR B 480 ARG 0.005 0.000 ARG D 456 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 443) hydrogen bonds : angle 4.70960 ( 1260) SS BOND : bond 0.00374 ( 6) SS BOND : angle 1.24811 ( 12) covalent geometry : bond 0.00255 (14306) covalent geometry : angle 0.56159 (19378) *********************** 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 109 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 67 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6786 (p0) REVERT: A 253 MET cc_start: 0.7915 (ttp) cc_final: 0.7440 (mtm) REVERT: A 342 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9284 (tt) REVERT: C 438 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8139 (ptm160) REVERT: C 454 GLU cc_start: 0.8415 (pp20) cc_final: 0.8097 (pp20) REVERT: D 110 MET cc_start: 0.9244 (ttt) cc_final: 0.8691 (ttt) REVERT: D 439 MET cc_start: 0.9574 (ttp) cc_final: 0.8848 (tmm) REVERT: D 701 MET cc_start: 0.8324 (tpp) cc_final: 0.7805 (tpp) REVERT: B 244 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7914 (mtp) REVERT: B 299 MET cc_start: 0.9401 (ttm) cc_final: 0.9045 (tpp) outliers start: 42 outliers final: 20 residues processed: 102 average time/residue: 0.2068 time to fit residues: 34.5523 Evaluate side-chains 89 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 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 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 594 TRP Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 131 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** 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 = 0.3249 r_free = 0.3249 target = 0.048850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035649 restraints weight = 84216.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036823 restraints weight = 41761.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037577 restraints weight = 27819.061| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14312 Z= 0.211 Angle : 0.621 11.003 19390 Z= 0.319 Chirality : 0.043 0.184 2121 Planarity : 0.004 0.060 2499 Dihedral : 4.537 23.643 1880 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.62 % Favored : 92.20 % Rotamer: Outliers : 2.71 % Allowed : 19.44 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.20), residues: 1719 helix: 1.46 (0.28), residues: 364 sheet: -0.55 (0.26), residues: 405 loop : -1.73 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 361 HIS 0.006 0.001 HIS D 706 PHE 0.013 0.001 PHE A 243 TYR 0.017 0.001 TYR E 244 ARG 0.008 0.001 ARG E 269 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 443) hydrogen bonds : angle 4.78055 ( 1260) SS BOND : bond 0.00318 ( 6) SS BOND : angle 1.48683 ( 12) covalent geometry : bond 0.00472 (14306) covalent geometry : angle 0.61989 (19378) *********************** 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 104 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6874 (p0) REVERT: A 253 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7868 (mtm) REVERT: A 342 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9283 (tt) REVERT: C 454 GLU cc_start: 0.8445 (pp20) cc_final: 0.8120 (pp20) REVERT: E 271 MET cc_start: 0.8465 (mpp) cc_final: 0.8262 (mpp) REVERT: D 110 MET cc_start: 0.9258 (ttt) cc_final: 0.8670 (ttt) REVERT: D 439 MET cc_start: 0.9559 (ttp) cc_final: 0.8861 (tmm) REVERT: D 701 MET cc_start: 0.8486 (tpp) cc_final: 0.8089 (tpp) REVERT: B 244 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.8003 (mtp) REVERT: B 299 MET cc_start: 0.9352 (ttm) cc_final: 0.9001 (tpp) outliers start: 41 outliers final: 26 residues processed: 93 average time/residue: 0.2118 time to fit residues: 33.0599 Evaluate side-chains 92 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 438 ARG Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 484 THR 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 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 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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 614 MET 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: 0.0000 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 HIS D 300 HIS ** B 655 ASN ** 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 = 0.3283 r_free = 0.3283 target = 0.050040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.036756 restraints weight = 83141.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.037983 restraints weight = 41030.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.038769 restraints weight = 26996.026| |-----------------------------------------------------------------------------| r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2881 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= 0.103 Angle : 0.546 10.201 19390 Z= 0.281 Chirality : 0.042 0.191 2121 Planarity : 0.004 0.058 2499 Dihedral : 4.299 20.615 1880 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.99 % Favored : 93.83 % Rotamer: Outliers : 1.98 % Allowed : 20.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1719 helix: 1.66 (0.28), residues: 365 sheet: -0.45 (0.27), residues: 395 loop : -1.61 (0.19), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 361 HIS 0.006 0.001 HIS A 176 PHE 0.013 0.001 PHE A 243 TYR 0.008 0.001 TYR A 21 ARG 0.004 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 443) hydrogen bonds : angle 4.43787 ( 1260) SS BOND : bond 0.00361 ( 6) SS BOND : angle 1.24212 ( 12) covalent geometry : bond 0.00228 (14306) covalent geometry : angle 0.54532 (19378) *********************** 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 93 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.7009 (p0) REVERT: A 253 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: A 342 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9260 (tt) REVERT: C 454 GLU cc_start: 0.8437 (pp20) cc_final: 0.8074 (pp20) REVERT: D 110 MET cc_start: 0.9305 (ttt) cc_final: 0.8692 (ttt) REVERT: D 439 MET cc_start: 0.9562 (ttp) cc_final: 0.8854 (tmm) REVERT: D 701 MET cc_start: 0.8466 (tpp) cc_final: 0.8061 (tpp) REVERT: B 244 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8021 (mtp) REVERT: B 299 MET cc_start: 0.9382 (ttm) cc_final: 0.8987 (tpp) REVERT: B 672 MET cc_start: 0.8991 (mmm) cc_final: 0.8465 (tmm) outliers start: 30 outliers final: 16 residues processed: 84 average time/residue: 0.2170 time to fit residues: 30.6942 Evaluate side-chains 81 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 395 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 462 VAL 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 594 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 556 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 149 optimal weight: 7.9990 chunk 172 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** 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 = 0.3258 r_free = 0.3258 target = 0.049145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035901 restraints weight = 83707.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.037082 restraints weight = 41570.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.037849 restraints weight = 27490.682| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.003 0.035 14312 Z= 0.150 Angle : 0.571 11.181 19390 Z= 0.292 Chirality : 0.042 0.179 2121 Planarity : 0.004 0.057 2499 Dihedral : 4.263 22.277 1880 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 2.65 % Allowed : 19.97 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1719 helix: 1.72 (0.28), residues: 364 sheet: -0.38 (0.27), residues: 394 loop : -1.55 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 361 HIS 0.006 0.001 HIS A 176 PHE 0.012 0.001 PHE A 243 TYR 0.013 0.001 TYR E 244 ARG 0.003 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 443) hydrogen bonds : angle 4.47563 ( 1260) SS BOND : bond 0.00310 ( 6) SS BOND : angle 1.32493 ( 12) covalent geometry : bond 0.00336 (14306) covalent geometry : angle 0.57051 (19378) *********************** 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 100 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 60 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7028 (p0) REVERT: A 253 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: A 342 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9254 (tt) REVERT: C 454 GLU cc_start: 0.8437 (pp20) cc_final: 0.8107 (pp20) REVERT: E 271 MET cc_start: 0.8636 (mpp) cc_final: 0.8375 (mpp) REVERT: D 110 MET cc_start: 0.9294 (ttt) cc_final: 0.8699 (ttt) REVERT: D 439 MET cc_start: 0.9558 (ttp) cc_final: 0.8884 (tmm) REVERT: D 701 MET cc_start: 0.8456 (tpp) cc_final: 0.8124 (tpp) REVERT: B 244 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: B 299 MET cc_start: 0.9378 (ttm) cc_final: 0.8985 (tpp) REVERT: B 672 MET cc_start: 0.9024 (mmm) cc_final: 0.8480 (tmm) outliers start: 40 outliers final: 21 residues processed: 89 average time/residue: 0.2480 time to fit residues: 36.8639 Evaluate side-chains 85 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 455 ASP Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 278 TYR Chi-restraints excluded: chain E residue 348 SER 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 594 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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 657 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 161 optimal weight: 0.0770 chunk 169 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** B 655 ASN ** 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 = 0.3264 r_free = 0.3264 target = 0.049383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.036148 restraints weight = 82354.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.037298 restraints weight = 40790.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.038066 restraints weight = 27111.962| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3238 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= 0.124 Angle : 0.557 11.815 19390 Z= 0.283 Chirality : 0.042 0.175 2121 Planarity : 0.004 0.060 2499 Dihedral : 4.221 21.779 1880 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.93 % Favored : 93.89 % Rotamer: Outliers : 2.38 % Allowed : 20.17 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1719 helix: 1.76 (0.29), residues: 364 sheet: -0.32 (0.27), residues: 408 loop : -1.54 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 361 HIS 0.006 0.001 HIS A 176 PHE 0.012 0.001 PHE A 243 TYR 0.010 0.001 TYR E 244 ARG 0.002 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.03438 ( 443) hydrogen bonds : angle 4.37901 ( 1260) SS BOND : bond 0.00327 ( 6) SS BOND : angle 1.27319 ( 12) covalent geometry : bond 0.00279 (14306) covalent geometry : angle 0.55644 (19378) *********************** 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 99 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6925 (p0) REVERT: A 253 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: A 342 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9270 (tt) REVERT: C 454 GLU cc_start: 0.8447 (pp20) cc_final: 0.8118 (pp20) REVERT: E 271 MET cc_start: 0.8595 (mpp) cc_final: 0.8317 (mpp) REVERT: D 110 MET cc_start: 0.9311 (ttt) cc_final: 0.8700 (ttt) REVERT: D 439 MET cc_start: 0.9546 (ttp) cc_final: 0.8813 (ppp) REVERT: D 701 MET cc_start: 0.8423 (tpp) cc_final: 0.8081 (tpp) REVERT: B 244 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7597 (mmm) REVERT: B 299 MET cc_start: 0.9357 (ttm) cc_final: 0.8958 (tpp) REVERT: B 672 MET cc_start: 0.9030 (mmm) cc_final: 0.8471 (tmm) outliers start: 36 outliers final: 25 residues processed: 90 average time/residue: 0.2044 time to fit residues: 31.3839 Evaluate side-chains 89 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 60 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 455 ASP 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 278 TYR Chi-restraints excluded: chain E residue 348 SER 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 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 29 optimal weight: 6.9990 chunk 161 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 131 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 374 GLN D 521 GLN ** B 655 ASN ** 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 = 0.3268 r_free = 0.3268 target = 0.049501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.036242 restraints weight = 82769.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037440 restraints weight = 41094.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.038200 restraints weight = 27116.010| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3392 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= 0.109 Angle : 0.545 12.311 19390 Z= 0.275 Chirality : 0.042 0.180 2121 Planarity : 0.004 0.063 2499 Dihedral : 4.108 20.897 1880 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.75 % Favored : 93.08 % Rotamer: Outliers : 2.05 % Allowed : 20.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1719 helix: 1.74 (0.28), residues: 367 sheet: -0.22 (0.27), residues: 416 loop : -1.44 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 361 HIS 0.006 0.001 HIS A 176 PHE 0.012 0.001 PHE A 243 TYR 0.010 0.001 TYR E 244 ARG 0.003 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 443) hydrogen bonds : angle 4.28468 ( 1260) SS BOND : bond 0.00345 ( 6) SS BOND : angle 1.23776 ( 12) covalent geometry : bond 0.00246 (14306) covalent geometry : angle 0.54437 (19378) *********************** 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 93 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6932 (p0) REVERT: A 253 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7849 (mtm) REVERT: A 342 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9270 (tt) REVERT: C 454 GLU cc_start: 0.8438 (pp20) cc_final: 0.8108 (pp20) REVERT: E 271 MET cc_start: 0.8590 (mpp) cc_final: 0.8289 (mpp) REVERT: D 110 MET cc_start: 0.9328 (ttt) cc_final: 0.8728 (ttt) REVERT: D 439 MET cc_start: 0.9523 (ttp) cc_final: 0.8793 (ppp) REVERT: D 701 MET cc_start: 0.8417 (tpp) cc_final: 0.8068 (tpp) REVERT: B 244 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: B 299 MET cc_start: 0.9394 (ttm) cc_final: 0.8951 (tpp) REVERT: B 672 MET cc_start: 0.9034 (mmm) cc_final: 0.8468 (tmm) outliers start: 31 outliers final: 21 residues processed: 86 average time/residue: 0.2158 time to fit residues: 30.7617 Evaluate side-chains 87 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 408 HIS Chi-restraints excluded: chain C residue 438 ARG Chi-restraints excluded: chain C residue 455 ASP 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 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 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 117 optimal weight: 0.0010 chunk 56 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 ASN ** D 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** 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 = 0.3290 r_free = 0.3290 target = 0.050233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.037063 restraints weight = 82635.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.038268 restraints weight = 40639.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.039040 restraints weight = 26707.107| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14312 Z= 0.091 Angle : 0.550 12.435 19390 Z= 0.274 Chirality : 0.042 0.189 2121 Planarity : 0.004 0.063 2499 Dihedral : 3.992 19.077 1880 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.12 % Rotamer: Outliers : 1.39 % Allowed : 20.90 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.21), residues: 1719 helix: 1.79 (0.28), residues: 368 sheet: -0.06 (0.27), residues: 409 loop : -1.39 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 361 HIS 0.005 0.001 HIS A 176 PHE 0.011 0.001 PHE D 32 TYR 0.007 0.001 TYR E 244 ARG 0.002 0.000 ARG B 682 Details of bonding type rmsd hydrogen bonds : bond 0.02954 ( 443) hydrogen bonds : angle 4.11968 ( 1260) SS BOND : bond 0.00388 ( 6) SS BOND : angle 1.14969 ( 12) covalent geometry : bond 0.00204 (14306) covalent geometry : angle 0.54906 (19378) ********************** 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 86 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.7189 (OUTLIER) cc_final: 0.6794 (p0) REVERT: A 253 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7796 (mtm) REVERT: A 342 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9284 (tt) REVERT: C 454 GLU cc_start: 0.8446 (pp20) cc_final: 0.8144 (pp20) REVERT: E 271 MET cc_start: 0.8578 (mpp) cc_final: 0.8294 (mpp) REVERT: D 110 MET cc_start: 0.9328 (ttt) cc_final: 0.8734 (ttt) REVERT: D 439 MET cc_start: 0.9515 (ttp) cc_final: 0.8785 (ppp) REVERT: D 701 MET cc_start: 0.8368 (tpp) cc_final: 0.7981 (tpp) REVERT: B 244 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8047 (mtp) REVERT: B 299 MET cc_start: 0.9393 (ttm) cc_final: 0.8945 (tpp) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.2397 time to fit residues: 31.2128 Evaluate side-chains 83 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.584 ------------------------------------------------------------------------------- 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 455 ASP Chi-restraints excluded: chain E residue 232 VAL 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 594 TRP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 556 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 31 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 106 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 0.0070 chunk 61 optimal weight: 0.1980 chunk 153 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 139 optimal weight: 0.0970 chunk 92 optimal weight: 0.8980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.050627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.037478 restraints weight = 83143.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038723 restraints weight = 40866.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.039516 restraints weight = 26698.438| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3654 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= 0.088 Angle : 0.534 12.134 19390 Z= 0.267 Chirality : 0.042 0.181 2121 Planarity : 0.004 0.062 2499 Dihedral : 3.846 18.707 1880 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.88 % Favored : 93.95 % Rotamer: Outliers : 1.46 % Allowed : 20.57 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.21), residues: 1719 helix: 1.85 (0.28), residues: 367 sheet: -0.06 (0.26), residues: 423 loop : -1.34 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 361 HIS 0.005 0.001 HIS A 176 PHE 0.011 0.001 PHE A 243 TYR 0.008 0.001 TYR E 244 ARG 0.003 0.000 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 443) hydrogen bonds : angle 4.01278 ( 1260) SS BOND : bond 0.00387 ( 6) SS BOND : angle 1.14354 ( 12) covalent geometry : bond 0.00196 (14306) covalent geometry : angle 0.53370 (19378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4855.58 seconds wall clock time: 88 minutes 49.45 seconds (5329.45 seconds total)