Starting phenix.real_space_refine on Fri Jun 13 15:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybr_39122/06_2025/8ybr_39122.cif" } resolution = 2.57 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= 0.026 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 66 5.16 5 C 9987 2.51 5 N 2472 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15150 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 9.03, per 1000 atoms: 0.60 Number of scatterers: 15150 At special positions: 0 Unit cell: (112.66, 115.24, 109.22, 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 66 16.00 O 2625 8.00 N 2472 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3522 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 7 sheets defined 74.7% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 removed outlier: 4.088A pdb=" N PHE A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 25 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.761A pdb=" N LEU A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 75 removed outlier: 3.738A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.607A pdb=" N LYS A 80 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.581A pdb=" N MET A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.718A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.578A pdb=" N ALA A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 3.687A pdb=" N TRP A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.775A pdb=" N ASN A 188 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 226 removed outlier: 3.817A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.957A pdb=" N GLN A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 304 removed outlier: 3.720A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.601A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.987A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 380 removed outlier: 3.891A pdb=" N ALA A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.676A pdb=" N GLY A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.747A pdb=" N ALA A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.567A pdb=" N VAL A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.514A pdb=" N VAL A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 460 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 3.848A pdb=" N VAL A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 514 removed outlier: 4.077A pdb=" N ILE A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.556A pdb=" N VAL A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 4.112A pdb=" N GLU A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.742A pdb=" N ALA A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 608 " --> pdb=" O SER A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 608' Processing helix chain 'A' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 36 removed outlier: 4.089A pdb=" N PHE B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 55 removed outlier: 3.763A pdb=" N LEU B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 75 removed outlier: 3.739A pdb=" N TYR B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 67 " --> pdb=" O MET B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.608A pdb=" N LYS B 80 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.582A pdb=" N MET B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.718A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.577A pdb=" N ALA B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.688A pdb=" N TRP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER B 177 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.775A pdb=" N ASN B 188 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 226 removed outlier: 3.819A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.957A pdb=" N GLN B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 304 removed outlier: 3.721A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.600A pdb=" N SER B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.988A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 380 removed outlier: 3.892A pdb=" N ALA B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.677A pdb=" N GLY B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 427 removed outlier: 3.745A pdb=" N ALA B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 removed outlier: 3.569A pdb=" N VAL B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.514A pdb=" N VAL B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 460 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 484 removed outlier: 3.849A pdb=" N VAL B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 514 removed outlier: 4.077A pdb=" N ILE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 534 through 536 No H-bonds generated for 'chain 'B' and resid 534 through 536' Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.554A pdb=" N VAL B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 548 " --> pdb=" O TYR B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 removed outlier: 4.113A pdb=" N GLU B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.742A pdb=" N ALA B 607 " --> pdb=" O PRO B 604 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 608 " --> pdb=" O SER B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 608' Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 36 removed outlier: 4.088A pdb=" N PHE C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.762A pdb=" N LEU C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 75 removed outlier: 3.738A pdb=" N TYR C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 67 " --> pdb=" O MET C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.608A pdb=" N LYS C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.580A pdb=" N MET C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.719A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.578A pdb=" N ALA C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 removed outlier: 3.687A pdb=" N TRP C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.774A pdb=" N ASN C 188 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 226 removed outlier: 3.819A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.958A pdb=" N GLN C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 246 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C 270 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 304 removed outlier: 3.721A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.600A pdb=" N SER C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Proline residue: C 333 - end of helix removed outlier: 3.986A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 380 removed outlier: 3.891A pdb=" N ALA C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.677A pdb=" N GLY C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 427 removed outlier: 3.746A pdb=" N ALA C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 421 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.568A pdb=" N VAL C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.513A pdb=" N VAL C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 460 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 484 removed outlier: 3.848A pdb=" N VAL C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 481 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 514 removed outlier: 4.076A pdb=" N ILE C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG C 508 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 509 " --> pdb=" O GLU C 505 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 528 through 533 Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.556A pdb=" N VAL C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 548 " --> pdb=" O TYR C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 564 removed outlier: 4.113A pdb=" N GLU C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.743A pdb=" N ALA C 607 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 608 " --> pdb=" O SER C 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 604 through 608' Processing helix chain 'C' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN C 647 " --> pdb=" O GLU C 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 651 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.593A pdb=" N ARG A 13 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 582 removed outlier: 3.518A pdb=" N VAL A 596 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.594A pdb=" N ARG B 13 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 568 through 569 removed outlier: 4.868A pdb=" N ASN B 568 " --> pdb=" O GLY B 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 580 through 582 removed outlier: 3.516A pdb=" N VAL B 596 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.594A pdb=" N ARG C 13 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.518A pdb=" N VAL C 596 " --> pdb=" O VAL C 580 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2082 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: 4.92 Time building geometry restraints manager: 4.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3864 1.33 - 1.45: 3251 1.45 - 1.57: 8353 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 15594 Sorted by residual: bond pdb=" CA VAL C 563 " pdb=" C VAL C 563 " ideal model delta sigma weight residual 1.524 1.487 0.037 1.22e-02 6.72e+03 9.28e+00 bond pdb=" CA LEU B 567 " pdb=" C LEU B 567 " ideal model delta sigma weight residual 1.523 1.559 -0.036 1.18e-02 7.18e+03 9.18e+00 bond pdb=" CA VAL B 563 " pdb=" C VAL B 563 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.40e+00 bond pdb=" CA VAL A 563 " pdb=" C VAL A 563 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.22e-02 6.72e+03 7.18e+00 bond pdb=" CA LEU A 567 " pdb=" C LEU A 567 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.31e-02 5.83e+03 6.55e+00 ... (remaining 15589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 20805 1.86 - 3.72: 371 3.72 - 5.59: 66 5.59 - 7.45: 13 7.45 - 9.31: 3 Bond angle restraints: 21258 Sorted by residual: angle pdb=" CA GLU B 643 " pdb=" CB GLU B 643 " pdb=" CG GLU B 643 " ideal model delta sigma weight residual 114.10 123.41 -9.31 2.00e+00 2.50e-01 2.17e+01 angle pdb=" CA GLU A 643 " pdb=" CB GLU A 643 " pdb=" CG GLU A 643 " ideal model delta sigma weight residual 114.10 123.40 -9.30 2.00e+00 2.50e-01 2.16e+01 angle pdb=" CA GLU C 643 " pdb=" CB GLU C 643 " pdb=" CG GLU C 643 " ideal model delta sigma weight residual 114.10 123.40 -9.30 2.00e+00 2.50e-01 2.16e+01 angle pdb=" N LYS B 565 " pdb=" CA LYS B 565 " pdb=" C LYS B 565 " ideal model delta sigma weight residual 112.99 106.46 6.53 1.61e+00 3.86e-01 1.64e+01 angle pdb=" CB GLU A 643 " pdb=" CG GLU A 643 " pdb=" CD GLU A 643 " ideal model delta sigma weight residual 112.60 119.21 -6.61 1.70e+00 3.46e-01 1.51e+01 ... (remaining 21253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8168 17.76 - 35.53: 562 35.53 - 53.29: 98 53.29 - 71.05: 16 71.05 - 88.81: 3 Dihedral angle restraints: 8847 sinusoidal: 3315 harmonic: 5532 Sorted by residual: dihedral pdb=" CA ASP A 255 " pdb=" C ASP A 255 " pdb=" N LYS A 256 " pdb=" CA LYS A 256 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP C 255 " pdb=" C ASP C 255 " pdb=" N LYS C 256 " pdb=" CA LYS C 256 " ideal model delta harmonic sigma weight residual -180.00 -152.31 -27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP B 255 " pdb=" C ASP B 255 " pdb=" N LYS B 256 " pdb=" CA LYS B 256 " ideal model delta harmonic sigma weight residual -180.00 -152.33 -27.67 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 8844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1126 0.027 - 0.055: 796 0.055 - 0.082: 305 0.082 - 0.109: 96 0.109 - 0.136: 47 Chirality restraints: 2370 Sorted by residual: chirality pdb=" CA PRO C 444 " pdb=" N PRO C 444 " pdb=" C PRO C 444 " pdb=" CB PRO C 444 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA VAL B 569 " pdb=" N VAL B 569 " pdb=" C VAL B 569 " pdb=" CB VAL B 569 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PRO A 444 " pdb=" N PRO A 444 " pdb=" C PRO A 444 " pdb=" CB PRO A 444 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 2367 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 562 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C PHE C 562 " 0.080 2.00e-02 2.50e+03 pdb=" O PHE C 562 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL C 563 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 562 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C PHE B 562 " 0.078 2.00e-02 2.50e+03 pdb=" O PHE B 562 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL B 563 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 562 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C PHE A 562 " 0.077 2.00e-02 2.50e+03 pdb=" O PHE A 562 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A 563 " -0.026 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3137 2.77 - 3.30: 13338 3.30 - 3.83: 22504 3.83 - 4.37: 27260 4.37 - 4.90: 48581 Nonbonded interactions: 114820 Sorted by model distance: nonbonded pdb=" NH2 ARG B 552 " pdb=" OD2 ASP B 574 " model vdw 2.237 3.120 nonbonded pdb=" NH2 ARG C 552 " pdb=" OD2 ASP C 574 " model vdw 2.238 3.120 nonbonded pdb=" NH2 ARG A 552 " pdb=" OD2 ASP A 574 " model vdw 2.239 3.120 nonbonded pdb=" OG SER A 576 " pdb=" OD1 ASP A 578 " model vdw 2.257 3.040 nonbonded pdb=" OG SER C 576 " pdb=" OD1 ASP C 578 " model vdw 2.258 3.040 ... (remaining 114815 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.430 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.760 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.005 0.046 15594 Z= 0.225 Angle : 0.674 9.309 21258 Z= 0.384 Chirality : 0.043 0.136 2370 Planarity : 0.005 0.046 2661 Dihedral : 12.453 88.814 5325 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.70 % Allowed : 4.47 % Favored : 94.83 % 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: -4.55 (0.15), residues: 1929 helix: -2.78 (0.11), residues: 1308 sheet: -2.88 (0.50), residues: 90 loop : -3.05 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 327 HIS 0.006 0.001 HIS B 217 PHE 0.013 0.001 PHE B 334 TYR 0.008 0.001 TYR C 640 ARG 0.008 0.001 ARG C 619 Details of bonding type rmsd hydrogen bonds : bond 0.22027 ( 718) hydrogen bonds : angle 6.34427 ( 2082) covalent geometry : bond 0.00483 (15594) covalent geometry : angle 0.67370 (21258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 391 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.7706 (tpt) cc_final: 0.6807 (tpt) REVERT: A 440 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8078 (ttpt) REVERT: A 529 GLN cc_start: 0.7860 (mp10) cc_final: 0.7510 (mp10) REVERT: A 556 ASP cc_start: 0.7398 (p0) cc_final: 0.7028 (p0) REVERT: A 629 SER cc_start: 0.7839 (m) cc_final: 0.7398 (t) REVERT: B 60 MET cc_start: 0.7990 (mmm) cc_final: 0.7406 (mmt) REVERT: B 94 TYR cc_start: 0.7301 (t80) cc_final: 0.7055 (t80) REVERT: B 134 GLU cc_start: 0.7163 (mp0) cc_final: 0.6960 (mp0) REVERT: B 263 ASP cc_start: 0.6785 (m-30) cc_final: 0.6520 (m-30) REVERT: B 529 GLN cc_start: 0.7758 (mp10) cc_final: 0.7481 (mp10) REVERT: B 625 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 29 PHE cc_start: 0.8132 (t80) cc_final: 0.7752 (t80) REVERT: C 230 HIS cc_start: 0.8298 (m-70) cc_final: 0.8097 (m-70) REVERT: C 440 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8074 (ttpt) REVERT: C 655 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7579 (ttm-80) outliers start: 11 outliers final: 4 residues processed: 394 average time/residue: 1.3645 time to fit residues: 585.7971 Evaluate side-chains 359 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 355 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 634 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 372 ASN A 509 GLN A 644 GLN A 647 ASN B 372 ASN B 509 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 49 ASN C 372 ASN C 509 GLN C 595 GLN C 647 ASN C 658 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102313 restraints weight = 21845.236| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.90 r_work: 0.3316 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15594 Z= 0.135 Angle : 0.559 5.539 21258 Z= 0.297 Chirality : 0.039 0.131 2370 Planarity : 0.005 0.056 2661 Dihedral : 4.737 30.489 2091 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.17 % Allowed : 12.77 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.14 (0.17), residues: 1929 helix: -1.72 (0.13), residues: 1341 sheet: -2.18 (0.48), residues: 90 loop : -2.54 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 661 PHE 0.016 0.001 PHE C 334 TYR 0.021 0.001 TYR C 621 ARG 0.008 0.001 ARG B 259 Details of bonding type rmsd hydrogen bonds : bond 0.05690 ( 718) hydrogen bonds : angle 3.99964 ( 2082) covalent geometry : bond 0.00302 (15594) covalent geometry : angle 0.55949 (21258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 1.623 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7180 (m-30) cc_final: 0.6918 (m-30) REVERT: A 621 TYR cc_start: 0.8261 (p90) cc_final: 0.7943 (p90) REVERT: B 60 MET cc_start: 0.8641 (mmm) cc_final: 0.8109 (mmt) REVERT: B 108 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7242 (mt) REVERT: B 134 GLU cc_start: 0.8138 (mp0) cc_final: 0.7844 (mp0) REVERT: B 259 ARG cc_start: 0.7009 (tpt-90) cc_final: 0.6700 (tmt-80) REVERT: B 558 VAL cc_start: 0.8356 (p) cc_final: 0.8144 (p) REVERT: C 440 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8241 (ttpt) REVERT: C 514 TYR cc_start: 0.7989 (m-80) cc_final: 0.7704 (m-80) REVERT: C 533 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8156 (tp-100) REVERT: C 621 TYR cc_start: 0.8380 (p90) cc_final: 0.8122 (p90) outliers start: 34 outliers final: 15 residues processed: 386 average time/residue: 1.3638 time to fit residues: 577.2657 Evaluate side-chains 367 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 351 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 32 optimal weight: 0.0060 chunk 38 optimal weight: 0.8980 chunk 159 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 658 GLN B 533 GLN B 627 HIS C 49 ASN C 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.116772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101413 restraints weight = 21521.443| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.89 r_work: 0.3300 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15594 Z= 0.161 Angle : 0.554 5.642 21258 Z= 0.293 Chirality : 0.041 0.143 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.410 26.192 2082 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.75 % Allowed : 13.98 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.30 (0.18), residues: 1929 helix: -1.07 (0.14), residues: 1347 sheet: -1.67 (0.48), residues: 90 loop : -2.32 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 PHE 0.019 0.001 PHE B 25 TYR 0.021 0.001 TYR B 621 ARG 0.008 0.001 ARG A 13 Details of bonding type rmsd hydrogen bonds : bond 0.06059 ( 718) hydrogen bonds : angle 3.86042 ( 2082) covalent geometry : bond 0.00385 (15594) covalent geometry : angle 0.55429 (21258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 361 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8345 (pt) cc_final: 0.8051 (mt) REVERT: A 82 LYS cc_start: 0.8376 (ttmt) cc_final: 0.8157 (ttmt) REVERT: A 108 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7071 (mt) REVERT: A 263 ASP cc_start: 0.7173 (m-30) cc_final: 0.6906 (m-30) REVERT: A 533 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8082 (tp-100) REVERT: A 542 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7275 (tm-30) REVERT: A 621 TYR cc_start: 0.8481 (p90) cc_final: 0.8229 (p90) REVERT: B 32 ILE cc_start: 0.8454 (pt) cc_final: 0.8181 (mt) REVERT: B 108 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7189 (mt) REVERT: B 134 GLU cc_start: 0.8130 (mp0) cc_final: 0.7808 (mp0) REVERT: B 478 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 621 TYR cc_start: 0.8328 (p90) cc_final: 0.8001 (p90) REVERT: C 32 ILE cc_start: 0.8563 (pt) cc_final: 0.8215 (mt) REVERT: C 514 TYR cc_start: 0.8047 (m-80) cc_final: 0.7751 (m-80) REVERT: C 533 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8178 (tp-100) outliers start: 43 outliers final: 20 residues processed: 376 average time/residue: 1.4052 time to fit residues: 577.0082 Evaluate side-chains 385 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 361 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 20 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 66 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.117442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.102015 restraints weight = 21221.055| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.87 r_work: 0.3308 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15594 Z= 0.144 Angle : 0.536 9.350 21258 Z= 0.283 Chirality : 0.040 0.135 2370 Planarity : 0.004 0.045 2661 Dihedral : 4.292 25.436 2082 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.68 % Allowed : 15.01 % Favored : 82.31 % 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: -1.78 (0.19), residues: 1929 helix: -0.70 (0.14), residues: 1347 sheet: -1.12 (0.52), residues: 84 loop : -2.14 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.005 0.001 HIS A 146 PHE 0.020 0.001 PHE C 334 TYR 0.019 0.001 TYR B 621 ARG 0.006 0.000 ARG B 655 Details of bonding type rmsd hydrogen bonds : bond 0.05510 ( 718) hydrogen bonds : angle 3.78326 ( 2082) covalent geometry : bond 0.00343 (15594) covalent geometry : angle 0.53562 (21258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 368 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8181 (m-30) cc_final: 0.7931 (m-30) REVERT: A 243 MET cc_start: 0.8068 (tpt) cc_final: 0.7478 (tpt) REVERT: A 263 ASP cc_start: 0.7169 (m-30) cc_final: 0.6890 (m-30) REVERT: A 437 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8461 (tp) REVERT: A 533 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8082 (tp-100) REVERT: A 542 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 108 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7103 (mt) REVERT: B 134 GLU cc_start: 0.8140 (mp0) cc_final: 0.7815 (mp0) REVERT: B 478 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 508 ARG cc_start: 0.7484 (ttp80) cc_final: 0.7232 (ttp80) REVERT: C 32 ILE cc_start: 0.8526 (pt) cc_final: 0.8284 (mt) REVERT: C 440 LYS cc_start: 0.8531 (ttpt) cc_final: 0.8274 (ttpp) REVERT: C 514 TYR cc_start: 0.8048 (m-80) cc_final: 0.7726 (m-80) REVERT: C 533 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8200 (tp-100) REVERT: C 542 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7375 (tm-30) REVERT: C 557 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7901 (tt0) outliers start: 42 outliers final: 21 residues processed: 385 average time/residue: 1.3348 time to fit residues: 562.8626 Evaluate side-chains 390 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 593 ILE Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 1 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 149 optimal weight: 0.0670 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.103086 restraints weight = 21417.708| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.89 r_work: 0.3319 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15594 Z= 0.121 Angle : 0.514 9.537 21258 Z= 0.270 Chirality : 0.039 0.130 2370 Planarity : 0.004 0.053 2661 Dihedral : 4.129 25.391 2082 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.68 % Allowed : 15.84 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.19), residues: 1929 helix: -0.28 (0.14), residues: 1341 sheet: -0.79 (0.53), residues: 84 loop : -2.07 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.022 0.001 PHE B 25 TYR 0.018 0.001 TYR B 621 ARG 0.011 0.001 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.04886 ( 718) hydrogen bonds : angle 3.67602 ( 2082) covalent geometry : bond 0.00281 (15594) covalent geometry : angle 0.51395 (21258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 367 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7105 (m-30) cc_final: 0.6825 (m-30) REVERT: A 437 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8457 (tp) REVERT: A 529 GLN cc_start: 0.8288 (pm20) cc_final: 0.8050 (mp10) REVERT: A 533 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8084 (tp-100) REVERT: A 542 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7431 (tm-30) REVERT: A 557 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8012 (tt0) REVERT: B 108 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7081 (mt) REVERT: B 134 GLU cc_start: 0.8169 (mp0) cc_final: 0.7849 (mp0) REVERT: B 478 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 557 GLU cc_start: 0.8345 (tt0) cc_final: 0.8128 (tt0) REVERT: C 29 PHE cc_start: 0.8448 (t80) cc_final: 0.8126 (t80) REVERT: C 325 TRP cc_start: 0.8478 (OUTLIER) cc_final: 0.7631 (m100) REVERT: C 440 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8371 (ttpp) REVERT: C 514 TYR cc_start: 0.8046 (m-80) cc_final: 0.7748 (m-80) REVERT: C 533 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8176 (tp-100) REVERT: C 557 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: C 619 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7814 (mmm160) outliers start: 42 outliers final: 20 residues processed: 388 average time/residue: 1.3055 time to fit residues: 554.7287 Evaluate side-chains 394 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 368 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 283 GLN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.117275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.101845 restraints weight = 21269.697| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.87 r_work: 0.3300 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15594 Z= 0.168 Angle : 0.562 10.058 21258 Z= 0.292 Chirality : 0.041 0.148 2370 Planarity : 0.004 0.044 2661 Dihedral : 4.162 25.100 2082 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.81 % Allowed : 16.79 % Favored : 80.40 % 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 (0.19), residues: 1929 helix: -0.17 (0.14), residues: 1347 sheet: -0.71 (0.53), residues: 84 loop : -2.06 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 PHE 0.023 0.001 PHE C 25 TYR 0.020 0.001 TYR B 621 ARG 0.007 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.05727 ( 718) hydrogen bonds : angle 3.76014 ( 2082) covalent geometry : bond 0.00410 (15594) covalent geometry : angle 0.56181 (21258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 379 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8629 (p) cc_final: 0.8348 (m) REVERT: A 243 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7877 (tpt) REVERT: A 263 ASP cc_start: 0.7135 (m-30) cc_final: 0.6852 (m-30) REVERT: A 393 ASP cc_start: 0.7945 (t0) cc_final: 0.7744 (t0) REVERT: A 437 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8486 (tp) REVERT: A 508 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7599 (ttp80) REVERT: A 529 GLN cc_start: 0.8227 (pm20) cc_final: 0.8014 (mp10) REVERT: A 533 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8073 (tp-100) REVERT: A 542 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 557 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8040 (tt0) REVERT: B 24 SER cc_start: 0.8509 (p) cc_final: 0.8294 (m) REVERT: B 108 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7084 (mt) REVERT: B 134 GLU cc_start: 0.8166 (mp0) cc_final: 0.7842 (mp0) REVERT: B 478 SER cc_start: 0.8337 (t) cc_final: 0.8065 (p) REVERT: B 542 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 29 PHE cc_start: 0.8476 (t80) cc_final: 0.8136 (t80) REVERT: C 88 ASP cc_start: 0.8176 (m-30) cc_final: 0.7930 (m-30) REVERT: C 306 ASP cc_start: 0.8547 (t0) cc_final: 0.8210 (t70) REVERT: C 331 TRP cc_start: 0.8768 (m100) cc_final: 0.8540 (m100) REVERT: C 440 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8388 (ttpp) REVERT: C 514 TYR cc_start: 0.8062 (m-80) cc_final: 0.7753 (m-80) REVERT: C 533 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8148 (tp-100) REVERT: C 557 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7876 (tt0) outliers start: 44 outliers final: 19 residues processed: 401 average time/residue: 1.3454 time to fit residues: 590.2447 Evaluate side-chains 401 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 377 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 102 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 119 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 283 GLN A 372 ASN C 49 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103866 restraints weight = 21301.832| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.88 r_work: 0.3330 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15594 Z= 0.109 Angle : 0.519 10.978 21258 Z= 0.269 Chirality : 0.038 0.135 2370 Planarity : 0.004 0.041 2661 Dihedral : 4.015 24.732 2082 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.98 % Allowed : 18.07 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.19), residues: 1929 helix: 0.15 (0.15), residues: 1347 sheet: -0.32 (0.54), residues: 84 loop : -1.99 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 PHE 0.027 0.001 PHE C 334 TYR 0.017 0.001 TYR B 621 ARG 0.008 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 718) hydrogen bonds : angle 3.62928 ( 2082) covalent geometry : bond 0.00244 (15594) covalent geometry : angle 0.51912 (21258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 375 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8602 (p) cc_final: 0.8350 (m) REVERT: A 224 TYR cc_start: 0.8709 (t80) cc_final: 0.8497 (t80) REVERT: A 263 ASP cc_start: 0.7101 (m-30) cc_final: 0.6822 (m-30) REVERT: A 325 TRP cc_start: 0.8322 (OUTLIER) cc_final: 0.7419 (m100) REVERT: A 437 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 508 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 529 GLN cc_start: 0.8210 (pm20) cc_final: 0.7976 (mp10) REVERT: A 533 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8090 (tp-100) REVERT: A 542 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7435 (tm-30) REVERT: A 557 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7977 (tt0) REVERT: B 24 SER cc_start: 0.8523 (p) cc_final: 0.8304 (m) REVERT: B 108 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7110 (mt) REVERT: B 134 GLU cc_start: 0.8154 (mp0) cc_final: 0.7833 (mp0) REVERT: B 325 TRP cc_start: 0.8522 (OUTLIER) cc_final: 0.7659 (m100) REVERT: B 478 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8080 (p) REVERT: C 29 PHE cc_start: 0.8508 (t80) cc_final: 0.8158 (t80) REVERT: C 88 ASP cc_start: 0.8217 (m-30) cc_final: 0.7946 (m-30) REVERT: C 134 GLU cc_start: 0.8004 (mp0) cc_final: 0.7705 (mp0) REVERT: C 306 ASP cc_start: 0.8529 (t0) cc_final: 0.8196 (t70) REVERT: C 325 TRP cc_start: 0.8446 (OUTLIER) cc_final: 0.7682 (m100) REVERT: C 440 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8374 (ttpp) REVERT: C 514 TYR cc_start: 0.8021 (m-80) cc_final: 0.7751 (m-80) REVERT: C 533 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8159 (tp-100) REVERT: C 557 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7885 (tt0) outliers start: 31 outliers final: 13 residues processed: 389 average time/residue: 1.4000 time to fit residues: 603.9576 Evaluate side-chains 397 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 377 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 0.0010 chunk 169 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.121117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105872 restraints weight = 21228.062| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.86 r_work: 0.3322 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15594 Z= 0.127 Angle : 0.540 11.672 21258 Z= 0.276 Chirality : 0.039 0.143 2370 Planarity : 0.004 0.041 2661 Dihedral : 3.979 24.388 2082 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.98 % Allowed : 18.52 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.52 (0.19), residues: 1929 helix: 0.28 (0.15), residues: 1350 sheet: -0.12 (0.54), residues: 84 loop : -1.96 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.025 0.001 PHE C 334 TYR 0.019 0.001 TYR B 621 ARG 0.008 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 718) hydrogen bonds : angle 3.63432 ( 2082) covalent geometry : bond 0.00298 (15594) covalent geometry : angle 0.54017 (21258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8609 (p) cc_final: 0.8360 (m) REVERT: A 96 SER cc_start: 0.8504 (m) cc_final: 0.8191 (p) REVERT: A 243 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7489 (tpt) REVERT: A 263 ASP cc_start: 0.7117 (m-30) cc_final: 0.6826 (m-30) REVERT: A 393 ASP cc_start: 0.7968 (t0) cc_final: 0.7754 (t0) REVERT: A 508 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7537 (ttp80) REVERT: A 529 GLN cc_start: 0.8194 (pm20) cc_final: 0.7975 (mp10) REVERT: A 533 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8094 (tp-100) REVERT: A 557 GLU cc_start: 0.8249 (tm-30) cc_final: 0.8009 (tt0) REVERT: B 24 SER cc_start: 0.8506 (p) cc_final: 0.8289 (m) REVERT: B 88 ASP cc_start: 0.8172 (m-30) cc_final: 0.7915 (m-30) REVERT: B 108 ILE cc_start: 0.7514 (OUTLIER) cc_final: 0.7108 (mt) REVERT: B 134 GLU cc_start: 0.8153 (mp0) cc_final: 0.7839 (mp0) REVERT: B 306 ASP cc_start: 0.8603 (t0) cc_final: 0.8348 (t70) REVERT: B 478 SER cc_start: 0.8336 (OUTLIER) cc_final: 0.8061 (p) REVERT: B 542 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 29 PHE cc_start: 0.8527 (t80) cc_final: 0.8129 (t80) REVERT: C 134 GLU cc_start: 0.8005 (mp0) cc_final: 0.7718 (mp0) REVERT: C 331 TRP cc_start: 0.8756 (m100) cc_final: 0.8547 (m100) REVERT: C 440 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8393 (ttpp) REVERT: C 514 TYR cc_start: 0.8033 (m-80) cc_final: 0.7755 (m-80) REVERT: C 533 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8149 (tp-100) REVERT: C 557 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7881 (tt0) outliers start: 31 outliers final: 18 residues processed: 396 average time/residue: 1.2771 time to fit residues: 554.2291 Evaluate side-chains 400 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 377 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 178 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.121114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.105852 restraints weight = 21202.414| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.85 r_work: 0.3322 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15594 Z= 0.129 Angle : 0.545 12.368 21258 Z= 0.281 Chirality : 0.039 0.147 2370 Planarity : 0.004 0.056 2661 Dihedral : 3.964 24.455 2082 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.17 % Allowed : 18.84 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.35 (0.19), residues: 1929 helix: 0.42 (0.15), residues: 1350 sheet: 0.04 (0.54), residues: 84 loop : -1.94 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.026 0.001 PHE C 334 TYR 0.019 0.001 TYR B 621 ARG 0.013 0.000 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 718) hydrogen bonds : angle 3.63940 ( 2082) covalent geometry : bond 0.00302 (15594) covalent geometry : angle 0.54470 (21258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 378 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8605 (p) cc_final: 0.8353 (m) REVERT: A 224 TYR cc_start: 0.8737 (t80) cc_final: 0.8531 (t80) REVERT: A 243 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7518 (tpt) REVERT: A 263 ASP cc_start: 0.7129 (m-30) cc_final: 0.6849 (m-30) REVERT: A 393 ASP cc_start: 0.7971 (t0) cc_final: 0.7753 (t0) REVERT: A 508 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7550 (ttp80) REVERT: A 533 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8119 (tp-100) REVERT: A 557 GLU cc_start: 0.8241 (tm-30) cc_final: 0.8013 (tt0) REVERT: B 108 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7110 (mt) REVERT: B 134 GLU cc_start: 0.8130 (mp0) cc_final: 0.7815 (mp0) REVERT: B 478 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8066 (p) REVERT: B 542 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7044 (tm-30) REVERT: C 29 PHE cc_start: 0.8518 (t80) cc_final: 0.8163 (t80) REVERT: C 88 ASP cc_start: 0.8205 (m-30) cc_final: 0.7960 (m-30) REVERT: C 306 ASP cc_start: 0.8514 (t0) cc_final: 0.8180 (t70) REVERT: C 331 TRP cc_start: 0.8760 (m100) cc_final: 0.8557 (m100) REVERT: C 514 TYR cc_start: 0.8036 (m-80) cc_final: 0.7755 (m-80) REVERT: C 533 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8157 (tp-100) REVERT: C 557 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7914 (tt0) outliers start: 34 outliers final: 22 residues processed: 395 average time/residue: 1.3155 time to fit residues: 570.2714 Evaluate side-chains 395 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 368 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.105205 restraints weight = 21377.820| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.88 r_work: 0.3315 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15594 Z= 0.147 Angle : 0.577 13.095 21258 Z= 0.293 Chirality : 0.040 0.150 2370 Planarity : 0.004 0.043 2661 Dihedral : 3.979 24.247 2082 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 19.03 % Favored : 79.25 % 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: -0.31 (0.19), residues: 1929 helix: 0.46 (0.15), residues: 1350 sheet: 0.10 (0.54), residues: 84 loop : -1.94 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.027 0.001 PHE C 25 TYR 0.019 0.001 TYR B 621 ARG 0.010 0.001 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.05158 ( 718) hydrogen bonds : angle 3.67053 ( 2082) covalent geometry : bond 0.00353 (15594) covalent geometry : angle 0.57681 (21258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 378 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8610 (p) cc_final: 0.8360 (m) REVERT: A 243 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7886 (tpt) REVERT: A 263 ASP cc_start: 0.7147 (m-30) cc_final: 0.6864 (m-30) REVERT: A 393 ASP cc_start: 0.8011 (t0) cc_final: 0.7794 (t0) REVERT: A 508 ARG cc_start: 0.7813 (ttp80) cc_final: 0.7568 (ttp80) REVERT: A 533 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8167 (tp-100) REVERT: A 557 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8008 (tt0) REVERT: B 108 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 134 GLU cc_start: 0.8133 (mp0) cc_final: 0.7821 (mp0) REVERT: B 478 SER cc_start: 0.8345 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 542 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7094 (tm-30) REVERT: C 29 PHE cc_start: 0.8522 (t80) cc_final: 0.8172 (t80) REVERT: C 88 ASP cc_start: 0.8233 (m-30) cc_final: 0.7976 (m-30) REVERT: C 134 GLU cc_start: 0.8010 (mp0) cc_final: 0.7723 (mp0) REVERT: C 306 ASP cc_start: 0.8520 (t0) cc_final: 0.8180 (t70) REVERT: C 331 TRP cc_start: 0.8764 (m100) cc_final: 0.8554 (m100) REVERT: C 450 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8161 (mtmm) REVERT: C 514 TYR cc_start: 0.8059 (m-80) cc_final: 0.7775 (m-80) REVERT: C 533 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8140 (tp-100) REVERT: C 557 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7917 (tt0) outliers start: 27 outliers final: 22 residues processed: 392 average time/residue: 1.2984 time to fit residues: 557.4263 Evaluate side-chains 402 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 375 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 159 optimal weight: 0.0980 chunk 63 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 43 optimal weight: 0.0170 chunk 186 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.121283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.105949 restraints weight = 21294.406| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.87 r_work: 0.3329 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15594 Z= 0.119 Angle : 0.552 13.251 21258 Z= 0.282 Chirality : 0.039 0.145 2370 Planarity : 0.004 0.090 2661 Dihedral : 3.948 24.183 2082 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.60 % Allowed : 19.35 % Favored : 79.05 % 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: -0.15 (0.20), residues: 1929 helix: 0.57 (0.15), residues: 1350 sheet: 0.25 (0.55), residues: 84 loop : -1.89 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 PHE 0.026 0.001 PHE C 334 TYR 0.018 0.001 TYR B 621 ARG 0.018 0.001 ARG C 655 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 718) hydrogen bonds : angle 3.62681 ( 2082) covalent geometry : bond 0.00272 (15594) covalent geometry : angle 0.55236 (21258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14862.66 seconds wall clock time: 256 minutes 29.13 seconds (15389.13 seconds total)