Starting phenix.real_space_refine on Mon Jan 20 11:25:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybr_39122/01_2025/8ybr_39122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybr_39122/01_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_39122/01_2025/8ybr_39122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybr_39122/01_2025/8ybr_39122.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybr_39122/01_2025/8ybr_39122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybr_39122/01_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.36, per 1000 atoms: 0.62 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: 3.69 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: 1.58 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: 4.84 Time building geometry restraints manager: 4.19 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: 0.10 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.360 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.740 ------------------------------------------------------------------------------- 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= 0.317 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 *********************** 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 : 1.791 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: 1.4181 time to fit residues: 609.2410 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 : 1.682 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102313 restraints weight = 21845.231| |-----------------------------------------------------------------------------| 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: 0.3179 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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= 0.197 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 *********************** 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 : 1.726 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7179 (m-30) cc_final: 0.6918 (m-30) REVERT: A 621 TYR cc_start: 0.8260 (p90) cc_final: 0.7942 (p90) REVERT: B 60 MET cc_start: 0.8642 (mmm) cc_final: 0.8112 (mmt) REVERT: B 108 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7242 (mt) REVERT: B 134 GLU cc_start: 0.8135 (mp0) cc_final: 0.7842 (mp0) REVERT: B 259 ARG cc_start: 0.7006 (tpt-90) cc_final: 0.6697 (tmt-80) REVERT: B 558 VAL cc_start: 0.8356 (p) cc_final: 0.8145 (p) REVERT: C 440 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8239 (ttpt) REVERT: C 514 TYR cc_start: 0.7986 (m-80) cc_final: 0.7700 (m-80) REVERT: C 533 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8157 (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: 1.3728 time to fit residues: 580.0996 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 : 1.815 ------------------------------------------------------------------------------- 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: 0.9990 chunk 161 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 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: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3621 r_free = 0.3621 target = 0.116870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.101452 restraints weight = 21471.188| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.89 r_work: 0.3302 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2463 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= 0.243 Angle : 0.555 5.636 21258 Z= 0.293 Chirality : 0.041 0.142 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.383 26.085 2082 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.75 % Allowed : 14.11 % Favored : 83.14 % 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: -2.22 (0.18), residues: 1929 helix: -1.00 (0.14), residues: 1344 sheet: -1.61 (0.48), residues: 90 loop : -2.32 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 PHE 0.023 0.001 PHE B 25 TYR 0.022 0.001 TYR B 621 ARG 0.009 0.001 ARG A 13 *********************** 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 400 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 357 time to evaluate : 1.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8333 (pt) cc_final: 0.8086 (mt) REVERT: A 82 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8168 (ttmt) REVERT: A 108 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 263 ASP cc_start: 0.7179 (m-30) cc_final: 0.6917 (m-30) REVERT: A 533 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8097 (tp-100) REVERT: A 542 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7337 (tm-30) REVERT: B 32 ILE cc_start: 0.8441 (pt) cc_final: 0.8198 (mt) REVERT: B 108 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7192 (mt) REVERT: B 134 GLU cc_start: 0.8132 (mp0) cc_final: 0.7810 (mp0) REVERT: B 478 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8097 (p) REVERT: B 508 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7321 (ttp80) REVERT: C 32 ILE cc_start: 0.8551 (pt) cc_final: 0.8245 (mt) REVERT: C 514 TYR cc_start: 0.8055 (m-80) cc_final: 0.7750 (m-80) REVERT: C 533 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8176 (tp-100) outliers start: 43 outliers final: 21 residues processed: 372 average time/residue: 1.4411 time to fit residues: 585.2094 Evaluate side-chains 385 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 360 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 393 ASP 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 191 ILE Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU 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: 0.9980 chunk 176 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.3046 ------------------------------------------------------------------------------- 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 C 170 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104104 restraints weight = 21264.123| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.88 r_work: 0.3339 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15594 Z= 0.142 Angle : 0.495 8.719 21258 Z= 0.261 Chirality : 0.038 0.134 2370 Planarity : 0.004 0.044 2661 Dihedral : 4.140 25.151 2082 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.30 % Allowed : 15.07 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1929 helix: -0.52 (0.14), residues: 1341 sheet: -0.84 (0.53), residues: 84 loop : -2.09 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 661 PHE 0.021 0.001 PHE C 334 TYR 0.019 0.001 TYR A 621 ARG 0.008 0.000 ARG C 655 *********************** 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 405 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8129 (tttt) REVERT: A 88 ASP cc_start: 0.8177 (m-30) cc_final: 0.7924 (m-30) REVERT: A 108 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7006 (mt) REVERT: A 263 ASP cc_start: 0.7108 (m-30) cc_final: 0.6835 (m-30) REVERT: A 334 PHE cc_start: 0.8201 (t80) cc_final: 0.7456 (t80) REVERT: A 367 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (mmt) REVERT: A 437 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 533 GLN cc_start: 0.8502 (tm130) cc_final: 0.8089 (tp-100) REVERT: A 542 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 108 ILE cc_start: 0.7508 (OUTLIER) cc_final: 0.7073 (mt) REVERT: B 134 GLU cc_start: 0.8137 (mp0) cc_final: 0.7812 (mp0) REVERT: B 325 TRP cc_start: 0.8499 (OUTLIER) cc_final: 0.7607 (m100) REVERT: B 478 SER cc_start: 0.8352 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 508 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7173 (ttp80) REVERT: B 621 TYR cc_start: 0.8343 (p90) cc_final: 0.7999 (p90) REVERT: C 440 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8298 (ttpp) REVERT: C 514 TYR cc_start: 0.7979 (m-80) cc_final: 0.7752 (m-10) REVERT: C 533 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8220 (tp-100) REVERT: C 542 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7379 (tm-30) REVERT: C 557 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7840 (tt0) outliers start: 36 outliers final: 10 residues processed: 382 average time/residue: 1.3396 time to fit residues: 560.8702 Evaluate side-chains 390 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 373 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET 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 367 MET Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 512 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 634 ASP Chi-restraints excluded: chain C residue 500 LYS 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: 0.0370 chunk 3 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 126 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 170 ASN A 283 GLN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN C 49 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.119007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.103718 restraints weight = 21439.470| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.86 r_work: 0.3289 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15594 Z= 0.304 Angle : 0.577 9.229 21258 Z= 0.301 Chirality : 0.042 0.136 2370 Planarity : 0.004 0.044 2661 Dihedral : 4.263 25.935 2082 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.81 % Allowed : 16.03 % Favored : 81.16 % 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: -1.41 (0.19), residues: 1929 helix: -0.36 (0.14), residues: 1338 sheet: -1.14 (0.50), residues: 90 loop : -2.18 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 327 HIS 0.006 0.001 HIS A 217 PHE 0.021 0.002 PHE C 334 TYR 0.018 0.002 TYR B 621 ARG 0.008 0.001 ARG C 655 *********************** 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 426 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 382 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7136 (m-30) cc_final: 0.6849 (m-30) REVERT: A 367 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (mmt) REVERT: A 393 ASP cc_start: 0.8008 (t0) cc_final: 0.7793 (t0) REVERT: A 505 GLU cc_start: 0.7919 (pt0) cc_final: 0.7706 (tt0) REVERT: A 529 GLN cc_start: 0.8261 (pm20) cc_final: 0.8006 (mp10) REVERT: A 533 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8062 (tp-100) REVERT: A 542 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7482 (tm-30) REVERT: A 557 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8074 (tt0) REVERT: B 24 SER cc_start: 0.8500 (p) cc_final: 0.8280 (m) REVERT: B 108 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7164 (mt) REVERT: B 134 GLU cc_start: 0.8160 (mp0) cc_final: 0.7841 (mp0) REVERT: B 478 SER cc_start: 0.8360 (t) cc_final: 0.8091 (p) REVERT: B 625 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 88 ASP cc_start: 0.8181 (m-30) cc_final: 0.7935 (m-30) REVERT: C 306 ASP cc_start: 0.8549 (t0) cc_final: 0.8204 (t70) REVERT: C 331 TRP cc_start: 0.8774 (m100) cc_final: 0.8573 (m100) REVERT: C 440 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8396 (ttpp) REVERT: C 514 TYR cc_start: 0.8068 (m-80) cc_final: 0.7766 (m-80) REVERT: C 533 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8145 (tp-100) REVERT: C 557 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7899 (tt0) outliers start: 44 outliers final: 20 residues processed: 404 average time/residue: 1.3395 time to fit residues: 592.8276 Evaluate side-chains 406 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 382 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 367 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 473 ILE 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 512 GLN Chi-restraints excluded: chain B residue 513 LEU 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 325 TRP Chi-restraints excluded: chain C residue 334 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 190 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.117952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102569 restraints weight = 21164.483| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.86 r_work: 0.3309 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15594 Z= 0.208 Angle : 0.534 9.682 21258 Z= 0.279 Chirality : 0.040 0.143 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.164 24.841 2082 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.36 % Allowed : 16.99 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.08 (0.19), residues: 1929 helix: -0.14 (0.14), residues: 1350 sheet: -0.65 (0.53), residues: 84 loop : -2.05 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 327 HIS 0.004 0.001 HIS A 217 PHE 0.025 0.001 PHE C 25 TYR 0.015 0.001 TYR B 621 ARG 0.010 0.000 ARG C 655 *********************** 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 420 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 383 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8618 (p) cc_final: 0.8335 (m) REVERT: A 243 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7284 (tpt) REVERT: A 263 ASP cc_start: 0.7139 (m-30) cc_final: 0.6854 (m-30) REVERT: A 393 ASP cc_start: 0.7998 (t0) cc_final: 0.7759 (t0) REVERT: A 505 GLU cc_start: 0.7865 (pt0) cc_final: 0.7660 (tt0) REVERT: A 529 GLN cc_start: 0.8214 (pm20) cc_final: 0.7992 (mp10) REVERT: A 533 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8103 (tp-100) REVERT: A 542 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7453 (tm-30) REVERT: A 557 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8087 (tt0) REVERT: B 24 SER cc_start: 0.8497 (p) cc_final: 0.8277 (m) REVERT: B 88 ASP cc_start: 0.8210 (m-30) cc_final: 0.7934 (m-30) REVERT: B 108 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 134 GLU cc_start: 0.8139 (mp0) cc_final: 0.7807 (mp0) REVERT: B 306 ASP cc_start: 0.8601 (t0) cc_final: 0.8350 (t70) REVERT: B 478 SER cc_start: 0.8339 (t) cc_final: 0.8070 (p) REVERT: B 508 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7248 (ttp80) REVERT: C 29 PHE cc_start: 0.8478 (t80) cc_final: 0.8122 (t80) REVERT: C 88 ASP cc_start: 0.8180 (m-30) cc_final: 0.7943 (m-30) REVERT: C 306 ASP cc_start: 0.8533 (t0) cc_final: 0.8195 (t70) REVERT: C 331 TRP cc_start: 0.8757 (m100) cc_final: 0.8545 (m100) REVERT: C 440 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8367 (ttpp) REVERT: C 514 TYR cc_start: 0.8055 (m-80) cc_final: 0.7741 (m-80) REVERT: C 533 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8159 (tp-100) REVERT: C 557 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7884 (tt0) outliers start: 37 outliers final: 22 residues processed: 402 average time/residue: 1.3494 time to fit residues: 595.2095 Evaluate side-chains 401 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 375 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 230 HIS 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 473 ILE 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 A residue 634 ASP 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 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 96 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 102 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 165 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.120467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.105115 restraints weight = 21323.095| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.86 r_work: 0.3308 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3108 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= 0.211 Angle : 0.548 11.027 21258 Z= 0.283 Chirality : 0.040 0.147 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.098 25.061 2082 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.75 % Allowed : 17.24 % Favored : 80.01 % 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: -0.82 (0.19), residues: 1929 helix: 0.06 (0.14), residues: 1350 sheet: -0.44 (0.53), residues: 84 loop : -2.01 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 PHE 0.023 0.001 PHE B 334 TYR 0.017 0.001 TYR B 621 ARG 0.010 0.000 ARG C 655 *********************** 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 421 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 378 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8615 (OUTLIER) cc_final: 0.8345 (m) REVERT: A 243 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7833 (tpt) REVERT: A 263 ASP cc_start: 0.7150 (m-30) cc_final: 0.6854 (m-30) REVERT: A 393 ASP cc_start: 0.8020 (t0) cc_final: 0.7779 (t0) REVERT: A 508 ARG cc_start: 0.7836 (ttp80) cc_final: 0.7602 (ttp80) REVERT: A 529 GLN cc_start: 0.8205 (pm20) cc_final: 0.8004 (mp10) REVERT: A 533 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8109 (tp-100) REVERT: A 542 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7495 (tm-30) REVERT: A 557 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8041 (tt0) REVERT: B 24 SER cc_start: 0.8477 (p) cc_final: 0.8266 (m) REVERT: B 108 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7100 (mt) REVERT: B 134 GLU cc_start: 0.8139 (mp0) cc_final: 0.7816 (mp0) REVERT: B 478 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8089 (p) REVERT: C 24 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8270 (m) REVERT: C 29 PHE cc_start: 0.8486 (t80) cc_final: 0.8125 (t80) REVERT: C 88 ASP cc_start: 0.8196 (m-30) cc_final: 0.7959 (m-30) REVERT: C 134 GLU cc_start: 0.8039 (mp0) cc_final: 0.7738 (mp0) REVERT: C 306 ASP cc_start: 0.8530 (t0) cc_final: 0.8205 (t70) REVERT: C 331 TRP cc_start: 0.8758 (m100) cc_final: 0.8545 (m100) REVERT: C 440 LYS cc_start: 0.8637 (ttpt) cc_final: 0.8379 (ttpp) REVERT: C 514 TYR cc_start: 0.8039 (m-80) cc_final: 0.7713 (m-80) REVERT: C 533 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8150 (tp-100) REVERT: C 557 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7904 (tt0) outliers start: 43 outliers final: 22 residues processed: 394 average time/residue: 1.3907 time to fit residues: 599.9215 Evaluate side-chains 405 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 376 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 230 HIS 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 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 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 462 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 516 LEU Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 75 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104616 restraints weight = 21136.367| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.85 r_work: 0.3301 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3183 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= 0.253 Angle : 0.571 11.504 21258 Z= 0.295 Chirality : 0.041 0.149 2370 Planarity : 0.004 0.046 2661 Dihedral : 4.122 24.809 2082 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.30 % Allowed : 18.01 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.76 (0.19), residues: 1929 helix: 0.14 (0.15), residues: 1350 sheet: -0.66 (0.50), residues: 90 loop : -2.07 (0.26), residues: 489 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 0.029 0.001 PHE C 25 TYR 0.017 0.001 TYR B 621 ARG 0.010 0.000 ARG C 655 *********************** 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 405 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 369 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8596 (p) cc_final: 0.8343 (m) REVERT: A 96 SER cc_start: 0.8502 (m) cc_final: 0.8178 (p) REVERT: A 243 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7883 (tpt) REVERT: A 263 ASP cc_start: 0.7170 (m-30) cc_final: 0.6891 (m-30) REVERT: A 393 ASP cc_start: 0.8081 (t0) cc_final: 0.7856 (t0) REVERT: A 533 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8110 (tp-100) REVERT: A 557 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8062 (tt0) REVERT: B 108 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7144 (mt) REVERT: B 134 GLU cc_start: 0.8139 (mp0) cc_final: 0.7829 (mp0) REVERT: B 478 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8074 (p) REVERT: B 542 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 29 PHE cc_start: 0.8489 (t80) cc_final: 0.8075 (t80) REVERT: C 88 ASP cc_start: 0.8222 (m-30) cc_final: 0.7976 (m-30) REVERT: C 134 GLU cc_start: 0.8028 (mp0) cc_final: 0.7751 (mp0) REVERT: C 306 ASP cc_start: 0.8531 (t0) cc_final: 0.8193 (t70) REVERT: C 331 TRP cc_start: 0.8768 (m100) cc_final: 0.8535 (m100) REVERT: C 514 TYR cc_start: 0.8064 (m-80) cc_final: 0.7733 (m-80) REVERT: C 533 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8131 (tp-100) REVERT: C 557 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7916 (tt0) outliers start: 36 outliers final: 24 residues processed: 385 average time/residue: 1.3436 time to fit residues: 566.0369 Evaluate side-chains 398 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 369 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 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 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 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 45 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 101 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 158 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 178 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.118152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103012 restraints weight = 21168.504| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.85 r_work: 0.3277 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15594 Z= 0.364 Angle : 0.629 12.379 21258 Z= 0.325 Chirality : 0.044 0.157 2370 Planarity : 0.004 0.049 2661 Dihedral : 4.297 25.564 2082 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.62 % Allowed : 18.01 % Favored : 79.37 % 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: -0.91 (0.19), residues: 1929 helix: 0.04 (0.14), residues: 1347 sheet: -0.82 (0.49), residues: 90 loop : -2.14 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 327 HIS 0.006 0.001 HIS A 217 PHE 0.028 0.002 PHE C 334 TYR 0.017 0.002 TYR B 621 ARG 0.008 0.001 ARG C 655 *********************** 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 422 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8344 (m) REVERT: A 393 ASP cc_start: 0.8144 (t0) cc_final: 0.7917 (t0) REVERT: A 533 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8121 (tm130) REVERT: A 557 GLU cc_start: 0.8324 (tm-30) cc_final: 0.8086 (tt0) REVERT: B 24 SER cc_start: 0.8441 (p) cc_final: 0.8220 (m) REVERT: B 88 ASP cc_start: 0.8174 (m-30) cc_final: 0.7887 (m-30) REVERT: B 108 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7137 (mt) REVERT: B 134 GLU cc_start: 0.8180 (mp0) cc_final: 0.7855 (mp0) REVERT: B 224 TYR cc_start: 0.8749 (t80) cc_final: 0.8499 (t80) REVERT: B 306 ASP cc_start: 0.8583 (t0) cc_final: 0.8334 (t70) REVERT: B 478 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8058 (p) REVERT: B 542 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 625 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7828 (mm-30) REVERT: C 29 PHE cc_start: 0.8497 (t80) cc_final: 0.8060 (t80) REVERT: C 88 ASP cc_start: 0.8217 (m-30) cc_final: 0.7955 (m-30) REVERT: C 306 ASP cc_start: 0.8540 (t0) cc_final: 0.8198 (t70) REVERT: C 331 TRP cc_start: 0.8773 (m100) cc_final: 0.8560 (m100) REVERT: C 450 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8155 (mtpp) REVERT: C 514 TYR cc_start: 0.8096 (m-80) cc_final: 0.7717 (m-80) REVERT: C 533 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8135 (tp-100) REVERT: C 619 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7799 (mmm160) outliers start: 41 outliers final: 30 residues processed: 399 average time/residue: 1.3704 time to fit residues: 599.1182 Evaluate side-chains 413 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 101 LEU 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 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain A residue 619 ARG Chi-restraints excluded: chain A residue 634 ASP 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 350 GLU 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 629 SER Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 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 643 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 54 optimal weight: 0.0370 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 163 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 overall best weight: 0.3436 ------------------------------------------------------------------------------- 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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106456 restraints weight = 21299.211| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.86 r_work: 0.3333 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.002 0.031 15594 Z= 0.156 Angle : 0.539 12.821 21258 Z= 0.276 Chirality : 0.038 0.138 2370 Planarity : 0.004 0.050 2661 Dihedral : 4.042 24.282 2082 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.66 % Allowed : 18.90 % Favored : 79.44 % 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: -0.43 (0.19), residues: 1929 helix: 0.38 (0.15), residues: 1350 sheet: -0.07 (0.53), residues: 84 loop : -2.00 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 327 HIS 0.004 0.001 HIS C 627 PHE 0.031 0.001 PHE C 334 TYR 0.015 0.001 TYR B 621 ARG 0.012 0.000 ARG C 655 ********************** 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 403 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 377 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8357 (m) REVERT: A 224 TYR cc_start: 0.8724 (t80) cc_final: 0.8518 (t80) REVERT: A 325 TRP cc_start: 0.8320 (OUTLIER) cc_final: 0.7505 (m100) REVERT: A 393 ASP cc_start: 0.8030 (t0) cc_final: 0.7802 (t0) REVERT: A 533 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8123 (tp-100) REVERT: A 557 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8023 (tt0) REVERT: B 24 SER cc_start: 0.8481 (p) cc_final: 0.8262 (m) REVERT: B 108 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7075 (mt) REVERT: B 134 GLU cc_start: 0.8136 (mp0) cc_final: 0.7818 (mp0) REVERT: B 325 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.7526 (m100) REVERT: B 478 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 542 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7141 (tm-30) REVERT: B 625 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 29 PHE cc_start: 0.8471 (t80) cc_final: 0.8024 (t80) REVERT: C 88 ASP cc_start: 0.8209 (m-30) cc_final: 0.7933 (m-30) REVERT: C 134 GLU cc_start: 0.8019 (mp0) cc_final: 0.7721 (mp0) REVERT: C 306 ASP cc_start: 0.8520 (t0) cc_final: 0.8190 (t70) REVERT: C 325 TRP cc_start: 0.8445 (OUTLIER) cc_final: 0.7684 (m100) REVERT: C 331 TRP cc_start: 0.8746 (m100) cc_final: 0.8540 (m100) REVERT: C 450 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8122 (mtpp) REVERT: C 514 TYR cc_start: 0.8039 (m-80) cc_final: 0.7746 (m-80) REVERT: C 533 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8137 (tp-100) outliers start: 26 outliers final: 17 residues processed: 391 average time/residue: 1.3679 time to fit residues: 585.5977 Evaluate side-chains 398 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 374 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 101 LEU 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 A residue 634 ASP 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 478 SER Chi-restraints excluded: chain B residue 506 SER 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 337 LEU Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 565 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 159 optimal weight: 0.0670 chunk 63 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 43 optimal weight: 0.0570 chunk 186 optimal weight: 0.8980 overall best weight: 0.3636 ------------------------------------------------------------------------------- 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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106527 restraints weight = 21232.950| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.87 r_work: 0.3336 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15594 Z= 0.156 Angle : 0.542 13.340 21258 Z= 0.276 Chirality : 0.038 0.139 2370 Planarity : 0.004 0.057 2661 Dihedral : 3.946 24.475 2082 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.40 % Allowed : 19.16 % Favored : 79.44 % 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: 0.58 (0.15), residues: 1347 sheet: 0.15 (0.55), residues: 84 loop : -1.88 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 PHE 0.034 0.001 PHE C 334 TYR 0.017 0.001 TYR B 621 ARG 0.013 0.000 ARG C 655 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13306.11 seconds wall clock time: 234 minutes 23.77 seconds (14063.77 seconds total)