Starting phenix.real_space_refine on Thu Sep 18 07:55:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybr_39122/09_2025/8ybr_39122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybr_39122/09_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_39122/09_2025/8ybr_39122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybr_39122/09_2025/8ybr_39122.map" model { file = "/net/cci-nas-00/data/ceres_data/8ybr_39122/09_2025/8ybr_39122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybr_39122/09_2025/8ybr_39122.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.16, per 1000 atoms: 0.27 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: 1.32 Conformation dependent library (CDL) restraints added in 808.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.69 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: 2.59 Time building geometry restraints manager: 1.84 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 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:8.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15594 Z= 0.225 Angle : 0.674 9.309 21258 Z= 0.384 Chirality : 0.043 0.136 2370 Planarity : 0.005 0.046 2661 Dihedral : 12.453 88.814 5325 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.58 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.008 0.001 ARG C 619 TYR 0.008 0.001 TYR C 640 PHE 0.013 0.001 PHE B 334 TRP 0.015 0.002 TRP B 327 HIS 0.006 0.001 HIS B 217 Details of bonding type rmsd covalent geometry : bond 0.00483 (15594) covalent geometry : angle 0.67370 (21258) hydrogen bonds : bond 0.22027 ( 718) hydrogen bonds : angle 6.34427 ( 2082) *********************** 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 : 0.611 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: 0.6929 time to fit residues: 296.8822 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 : 0.592 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0060 overall best weight: 0.3112 ------------------------------------------------------------------------------- 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 644 GLN C 647 ASN C 658 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.118826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103186 restraints weight = 21799.278| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.89 r_work: 0.3333 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15594 Z= 0.120 Angle : 0.534 5.611 21258 Z= 0.284 Chirality : 0.038 0.128 2370 Planarity : 0.004 0.046 2661 Dihedral : 4.713 30.282 2091 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.17 % Allowed : 12.71 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.17), residues: 1929 helix: -1.69 (0.13), residues: 1323 sheet: -2.15 (0.49), residues: 90 loop : -2.43 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 259 TYR 0.019 0.001 TYR C 621 PHE 0.017 0.001 PHE C 334 TRP 0.015 0.001 TRP B 327 HIS 0.004 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00248 (15594) covalent geometry : angle 0.53423 (21258) hydrogen bonds : bond 0.05662 ( 718) hydrogen bonds : angle 4.01705 ( 2082) *********************** 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 412 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 378 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8300 (m-30) cc_final: 0.8098 (m-30) REVERT: A 263 ASP cc_start: 0.7163 (m-30) cc_final: 0.6908 (m-30) REVERT: A 325 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.7721 (m100) REVERT: A 621 TYR cc_start: 0.8117 (p90) cc_final: 0.7673 (p90) REVERT: B 60 MET cc_start: 0.8619 (mmm) cc_final: 0.8116 (mmt) REVERT: B 61 MET cc_start: 0.8450 (tpp) cc_final: 0.8240 (tpp) REVERT: B 108 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7258 (mt) REVERT: B 134 GLU cc_start: 0.8145 (mp0) cc_final: 0.7847 (mp0) REVERT: B 325 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.7771 (m100) REVERT: B 558 VAL cc_start: 0.8309 (p) cc_final: 0.8102 (p) REVERT: C 325 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.7764 (m100) REVERT: C 440 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8213 (ttpt) REVERT: C 514 TYR cc_start: 0.7939 (m-80) cc_final: 0.7666 (m-80) REVERT: C 533 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8142 (tp-100) REVERT: C 621 TYR cc_start: 0.8238 (p90) cc_final: 0.8023 (p90) outliers start: 34 outliers final: 13 residues processed: 391 average time/residue: 0.6624 time to fit residues: 282.7182 Evaluate side-chains 374 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 357 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 191 ILE 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 589 GLU Chi-restraints excluded: chain B residue 31 ILE 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 24 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 166 optimal weight: 0.9990 chunk 157 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 C 49 ASN C 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.118375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.102793 restraints weight = 21859.473| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.90 r_work: 0.3324 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15594 Z= 0.122 Angle : 0.522 6.234 21258 Z= 0.275 Chirality : 0.039 0.142 2370 Planarity : 0.004 0.041 2661 Dihedral : 4.310 25.687 2084 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.81 % Allowed : 14.30 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.18), residues: 1929 helix: -1.05 (0.14), residues: 1344 sheet: -1.22 (0.52), residues: 84 loop : -2.28 (0.25), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 540 TYR 0.021 0.001 TYR B 621 PHE 0.026 0.001 PHE C 334 TRP 0.016 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00278 (15594) covalent geometry : angle 0.52199 (21258) hydrogen bonds : bond 0.05123 ( 718) hydrogen bonds : angle 3.78149 ( 2082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8310 (pt) cc_final: 0.8015 (mt) REVERT: A 263 ASP cc_start: 0.7104 (m-30) cc_final: 0.6862 (m-30) REVERT: A 325 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.7631 (m100) REVERT: A 542 GLU cc_start: 0.7337 (tm-30) cc_final: 0.7122 (tm-30) REVERT: A 544 TYR cc_start: 0.7839 (m-80) cc_final: 0.7445 (m-80) REVERT: A 621 TYR cc_start: 0.8268 (p90) cc_final: 0.7872 (p90) REVERT: B 60 MET cc_start: 0.8670 (mmm) cc_final: 0.8080 (mmt) REVERT: B 108 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7244 (mt) REVERT: B 134 GLU cc_start: 0.8157 (mp0) cc_final: 0.7831 (mp0) REVERT: C 325 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.7747 (m100) REVERT: C 440 LYS cc_start: 0.8549 (ttpt) cc_final: 0.8310 (ttpt) REVERT: C 514 TYR cc_start: 0.7974 (m-80) cc_final: 0.7724 (m-80) REVERT: C 533 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8177 (tp-100) REVERT: C 557 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: C 621 TYR cc_start: 0.8408 (p90) cc_final: 0.8163 (p90) outliers start: 44 outliers final: 19 residues processed: 373 average time/residue: 0.6849 time to fit residues: 278.0254 Evaluate side-chains 371 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 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 512 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 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 C residue 45 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 11 optimal weight: 0.0980 chunk 86 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 627 HIS C 49 ASN C 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.102386 restraints weight = 21708.862| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.90 r_work: 0.3314 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15594 Z= 0.136 Angle : 0.528 9.844 21258 Z= 0.278 Chirality : 0.040 0.148 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.213 25.310 2082 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.62 % Allowed : 15.07 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.19), residues: 1929 helix: -0.65 (0.14), residues: 1341 sheet: -0.79 (0.53), residues: 84 loop : -2.12 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 655 TYR 0.021 0.001 TYR B 621 PHE 0.018 0.001 PHE C 25 TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00319 (15594) covalent geometry : angle 0.52816 (21258) hydrogen bonds : bond 0.05202 ( 718) hydrogen bonds : angle 3.73590 ( 2082) *********************** 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 398 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 357 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7126 (m-30) cc_final: 0.6855 (m-30) REVERT: A 367 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (mmt) REVERT: A 533 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8090 (tp-100) REVERT: A 542 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 544 TYR cc_start: 0.7937 (m-80) cc_final: 0.7623 (m-80) REVERT: A 621 TYR cc_start: 0.8437 (p90) cc_final: 0.8133 (p90) REVERT: B 108 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7208 (mt) REVERT: B 134 GLU cc_start: 0.8158 (mp0) cc_final: 0.7824 (mp0) REVERT: B 478 SER cc_start: 0.8407 (OUTLIER) cc_final: 0.8100 (p) REVERT: C 32 ILE cc_start: 0.8523 (pt) cc_final: 0.8250 (mt) REVERT: C 514 TYR cc_start: 0.8002 (m-80) cc_final: 0.7719 (m-80) REVERT: C 533 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8158 (tp-100) REVERT: C 557 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: C 619 ARG cc_start: 0.8363 (mtt180) cc_final: 0.8055 (mmm160) outliers start: 41 outliers final: 21 residues processed: 370 average time/residue: 0.6798 time to fit residues: 274.2550 Evaluate side-chains 377 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 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 350 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 437 LEU 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 478 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU 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 283 GLN Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 599 LYS 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 75 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102166 restraints weight = 21466.654| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.89 r_work: 0.3308 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15594 Z= 0.144 Angle : 0.537 9.291 21258 Z= 0.282 Chirality : 0.040 0.141 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.181 25.793 2082 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.62 % Allowed : 15.26 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 1929 helix: -0.37 (0.14), residues: 1338 sheet: -0.58 (0.55), residues: 84 loop : -2.10 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 655 TYR 0.020 0.001 TYR B 621 PHE 0.023 0.001 PHE B 25 TRP 0.017 0.001 TRP B 327 HIS 0.006 0.001 HIS C 284 Details of bonding type rmsd covalent geometry : bond 0.00343 (15594) covalent geometry : angle 0.53711 (21258) hydrogen bonds : bond 0.05382 ( 718) hydrogen bonds : angle 3.72906 ( 2082) *********************** 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 414 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 373 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7255 (tpt) REVERT: A 263 ASP cc_start: 0.7138 (m-30) cc_final: 0.6855 (m-30) REVERT: A 367 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (mmt) REVERT: A 437 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 505 GLU cc_start: 0.7877 (pt0) cc_final: 0.7672 (tt0) REVERT: A 533 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8086 (tp-100) REVERT: A 542 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7349 (tm-30) REVERT: A 557 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8066 (tt0) REVERT: B 108 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7133 (mt) REVERT: B 134 GLU cc_start: 0.8137 (mp0) cc_final: 0.7812 (mp0) REVERT: B 478 SER cc_start: 0.8397 (OUTLIER) cc_final: 0.8109 (p) REVERT: B 508 ARG cc_start: 0.7543 (ttp80) cc_final: 0.7308 (ttp80) REVERT: B 532 SER cc_start: 0.8411 (p) cc_final: 0.8155 (p) REVERT: B 621 TYR cc_start: 0.8301 (p90) cc_final: 0.8011 (p90) REVERT: C 440 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8264 (ttpp) REVERT: C 514 TYR cc_start: 0.8044 (m-80) cc_final: 0.7730 (m-80) REVERT: C 533 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8174 (tp-100) REVERT: C 557 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: C 619 ARG cc_start: 0.8371 (mtt180) cc_final: 0.8170 (mmm160) outliers start: 41 outliers final: 23 residues processed: 387 average time/residue: 0.6849 time to fit residues: 288.9427 Evaluate side-chains 388 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 358 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE 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 350 GLU Chi-restraints excluded: chain A residue 367 MET 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 B residue 108 ILE Chi-restraints excluded: chain B residue 243 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 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 96 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 140 optimal weight: 0.3980 chunk 143 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 137 optimal weight: 0.1980 chunk 96 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103679 restraints weight = 21455.558| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.89 r_work: 0.3332 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15594 Z= 0.110 Angle : 0.513 9.705 21258 Z= 0.266 Chirality : 0.039 0.133 2370 Planarity : 0.004 0.051 2661 Dihedral : 4.026 24.657 2082 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.11 % Allowed : 16.86 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.19), residues: 1929 helix: -0.00 (0.15), residues: 1338 sheet: -0.30 (0.55), residues: 84 loop : -2.06 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 540 TYR 0.019 0.001 TYR B 621 PHE 0.028 0.001 PHE C 334 TRP 0.017 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00250 (15594) covalent geometry : angle 0.51281 (21258) hydrogen bonds : bond 0.04456 ( 718) hydrogen bonds : angle 3.61195 ( 2082) *********************** 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 398 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7079 (m-30) cc_final: 0.6804 (m-30) REVERT: A 325 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7533 (m100) REVERT: A 437 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8415 (tp) REVERT: A 508 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7582 (ttp80) REVERT: A 529 GLN cc_start: 0.8270 (pm20) cc_final: 0.8009 (mp10) REVERT: A 533 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8092 (tp-100) REVERT: A 542 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7455 (tm-30) REVERT: A 557 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8008 (tt0) REVERT: B 24 SER cc_start: 0.8530 (p) cc_final: 0.8307 (m) REVERT: B 108 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7093 (mt) REVERT: B 134 GLU cc_start: 0.8153 (mp0) cc_final: 0.7831 (mp0) REVERT: B 325 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7650 (m100) REVERT: B 478 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8090 (p) REVERT: B 508 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7281 (ttp80) REVERT: B 532 SER cc_start: 0.8419 (p) cc_final: 0.8150 (p) REVERT: B 621 TYR cc_start: 0.8339 (p90) cc_final: 0.8004 (p90) REVERT: C 29 PHE cc_start: 0.8459 (t80) cc_final: 0.8109 (t80) REVERT: C 88 ASP cc_start: 0.8193 (m-30) cc_final: 0.7977 (m-30) REVERT: C 306 ASP cc_start: 0.8530 (t0) cc_final: 0.8188 (t70) REVERT: C 325 TRP cc_start: 0.8428 (OUTLIER) cc_final: 0.7669 (m100) REVERT: C 440 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8366 (ttpp) REVERT: C 514 TYR cc_start: 0.8005 (m-80) cc_final: 0.7761 (m-80) REVERT: C 533 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8180 (tp-100) REVERT: C 557 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7877 (tt0) outliers start: 33 outliers final: 14 residues processed: 379 average time/residue: 0.6322 time to fit residues: 262.1685 Evaluate side-chains 375 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 353 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 248 LEU 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 350 GLU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain 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 478 SER Chi-restraints excluded: chain B residue 506 SER 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 325 TRP Chi-restraints excluded: chain C residue 557 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 155 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B 533 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.117583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.102069 restraints weight = 21016.912| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.87 r_work: 0.3304 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15594 Z= 0.162 Angle : 0.562 10.737 21258 Z= 0.292 Chirality : 0.041 0.143 2370 Planarity : 0.004 0.041 2661 Dihedral : 4.102 25.166 2082 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.49 % Allowed : 17.75 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.19), residues: 1929 helix: 0.07 (0.14), residues: 1347 sheet: -0.23 (0.54), residues: 84 loop : -2.01 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 186 TYR 0.018 0.001 TYR B 621 PHE 0.027 0.001 PHE C 334 TRP 0.015 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00392 (15594) covalent geometry : angle 0.56165 (21258) hydrogen bonds : bond 0.05617 ( 718) hydrogen bonds : angle 3.73145 ( 2082) *********************** 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 408 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 369 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASP cc_start: 0.7100 (m-30) cc_final: 0.6812 (m-30) REVERT: A 437 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8445 (tp) REVERT: A 440 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8204 (ttpp) REVERT: A 508 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7619 (ttp80) REVERT: A 529 GLN cc_start: 0.8241 (pm20) cc_final: 0.7982 (mp10) REVERT: A 533 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8075 (tp-100) REVERT: A 542 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 557 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8038 (tt0) REVERT: B 24 SER cc_start: 0.8506 (p) cc_final: 0.8293 (m) REVERT: B 88 ASP cc_start: 0.8217 (m-30) cc_final: 0.7973 (m-30) REVERT: B 108 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7090 (mt) REVERT: B 134 GLU cc_start: 0.8156 (mp0) cc_final: 0.7841 (mp0) REVERT: B 306 ASP cc_start: 0.8608 (t0) cc_final: 0.8351 (t70) REVERT: B 478 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8071 (p) REVERT: B 532 SER cc_start: 0.8445 (p) cc_final: 0.8170 (p) REVERT: C 29 PHE cc_start: 0.8476 (t80) cc_final: 0.8126 (t80) REVERT: C 440 LYS cc_start: 0.8632 (ttpt) cc_final: 0.8394 (ttpp) REVERT: C 514 TYR cc_start: 0.8011 (m-80) cc_final: 0.7705 (m-80) REVERT: C 533 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8146 (tp-100) REVERT: C 557 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7911 (tt0) REVERT: C 619 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8084 (mmm160) outliers start: 39 outliers final: 16 residues processed: 385 average time/residue: 0.6429 time to fit residues: 270.5783 Evaluate side-chains 389 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 367 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 619 ARG 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 143 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.120409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.105055 restraints weight = 21314.975| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.86 r_work: 0.3309 rms_B_bonded: 2.23 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: 0.8184 moved from start: 0.3127 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= 0.151 Angle : 0.567 11.787 21258 Z= 0.292 Chirality : 0.041 0.141 2370 Planarity : 0.004 0.057 2661 Dihedral : 4.085 24.429 2082 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.79 % Allowed : 18.58 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.19), residues: 1929 helix: 0.21 (0.15), residues: 1347 sheet: -0.06 (0.55), residues: 84 loop : -1.99 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 655 TYR 0.019 0.001 TYR B 621 PHE 0.031 0.001 PHE C 334 TRP 0.017 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00363 (15594) covalent geometry : angle 0.56745 (21258) hydrogen bonds : bond 0.05366 ( 718) hydrogen bonds : angle 3.71103 ( 2082) *********************** 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 395 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 367 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8625 (p) cc_final: 0.8338 (m) REVERT: A 225 LEU cc_start: 0.8506 (mt) cc_final: 0.8284 (mp) REVERT: A 263 ASP cc_start: 0.7106 (m-30) cc_final: 0.6828 (m-30) REVERT: A 440 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8246 (ttpp) REVERT: A 529 GLN cc_start: 0.8197 (pm20) cc_final: 0.7959 (mp10) REVERT: A 533 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8102 (tp-100) REVERT: A 542 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 557 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7909 (tt0) REVERT: B 24 SER cc_start: 0.8477 (p) cc_final: 0.8257 (m) REVERT: B 108 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7071 (mt) REVERT: B 134 GLU cc_start: 0.8161 (mp0) cc_final: 0.7847 (mp0) REVERT: B 478 SER cc_start: 0.8342 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 532 SER cc_start: 0.8424 (p) cc_final: 0.8159 (p) REVERT: C 29 PHE cc_start: 0.8518 (t80) cc_final: 0.8153 (t80) REVERT: C 88 ASP cc_start: 0.8194 (m-30) cc_final: 0.7936 (m-30) REVERT: C 134 GLU cc_start: 0.8050 (mp0) cc_final: 0.7730 (mp0) REVERT: C 306 ASP cc_start: 0.8523 (t0) cc_final: 0.8184 (t70) REVERT: C 440 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8388 (ttpp) REVERT: C 514 TYR cc_start: 0.8040 (m-80) cc_final: 0.7727 (m-80) REVERT: C 533 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8137 (tp-100) REVERT: C 557 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: C 619 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8182 (mmm-85) outliers start: 28 outliers final: 18 residues processed: 378 average time/residue: 0.6696 time to fit residues: 276.1262 Evaluate side-chains 388 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 365 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 544 TYR 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 243 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 C residue 325 TRP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 619 ARG 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 4 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 chunk 57 optimal weight: 0.0770 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105595 restraints weight = 21080.620| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.84 r_work: 0.3321 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3188 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= 0.130 Angle : 0.554 12.247 21258 Z= 0.286 Chirality : 0.040 0.141 2370 Planarity : 0.004 0.089 2661 Dihedral : 4.027 24.563 2082 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.60 % Allowed : 19.48 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.19), residues: 1929 helix: 0.36 (0.15), residues: 1350 sheet: 0.13 (0.56), residues: 84 loop : -1.99 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 655 TYR 0.019 0.001 TYR B 621 PHE 0.031 0.001 PHE C 334 TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00305 (15594) covalent geometry : angle 0.55435 (21258) hydrogen bonds : bond 0.04967 ( 718) hydrogen bonds : angle 3.68093 ( 2082) *********************** 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 392 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 367 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8614 (p) cc_final: 0.8331 (m) REVERT: A 96 SER cc_start: 0.8509 (m) cc_final: 0.8180 (p) REVERT: A 224 TYR cc_start: 0.8728 (t80) cc_final: 0.8521 (t80) REVERT: A 440 LYS cc_start: 0.8533 (ttpt) cc_final: 0.8235 (ttpp) REVERT: A 529 GLN cc_start: 0.8178 (pm20) cc_final: 0.7965 (mp10) REVERT: A 533 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8127 (tp-100) REVERT: A 557 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7888 (tt0) REVERT: B 24 SER cc_start: 0.8472 (p) cc_final: 0.8254 (m) REVERT: B 108 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7068 (mt) REVERT: B 134 GLU cc_start: 0.8138 (mp0) cc_final: 0.7826 (mp0) REVERT: B 478 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.8058 (p) REVERT: B 532 SER cc_start: 0.8423 (p) cc_final: 0.8173 (p) REVERT: C 29 PHE cc_start: 0.8505 (t80) cc_final: 0.8130 (t80) REVERT: C 88 ASP cc_start: 0.8231 (m-30) cc_final: 0.7973 (m-30) REVERT: C 134 GLU cc_start: 0.8039 (mp0) cc_final: 0.7761 (mp0) REVERT: C 306 ASP cc_start: 0.8508 (t0) cc_final: 0.8175 (t70) REVERT: C 450 LYS cc_start: 0.8361 (ptpp) cc_final: 0.8043 (mtpp) REVERT: C 514 TYR cc_start: 0.8013 (m-80) cc_final: 0.7737 (m-80) REVERT: C 533 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8138 (tp-100) REVERT: C 557 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7902 (tt0) outliers start: 25 outliers final: 15 residues processed: 377 average time/residue: 0.6764 time to fit residues: 278.6697 Evaluate side-chains 383 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 364 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 90 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 133 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.120555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105181 restraints weight = 21257.266| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.87 r_work: 0.3313 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15594 Z= 0.149 Angle : 0.575 12.954 21258 Z= 0.294 Chirality : 0.041 0.153 2370 Planarity : 0.004 0.041 2661 Dihedral : 4.026 24.351 2082 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.66 % Allowed : 19.67 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.19), residues: 1929 helix: 0.41 (0.15), residues: 1347 sheet: -0.17 (0.54), residues: 90 loop : -2.00 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 186 TYR 0.019 0.001 TYR B 621 PHE 0.031 0.001 PHE C 334 TRP 0.016 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00359 (15594) covalent geometry : angle 0.57515 (21258) hydrogen bonds : bond 0.05285 ( 718) hydrogen bonds : angle 3.70521 ( 2082) ********************** 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 402 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 376 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8614 (p) cc_final: 0.8334 (m) REVERT: A 440 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8239 (ttpp) REVERT: A 508 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7547 (ttp80) REVERT: A 529 GLN cc_start: 0.8182 (pm20) cc_final: 0.7965 (mp10) REVERT: A 533 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8159 (tp-100) REVERT: A 557 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7890 (tt0) REVERT: B 88 ASP cc_start: 0.8171 (m-30) cc_final: 0.7945 (m-30) REVERT: B 108 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7066 (mt) REVERT: B 134 GLU cc_start: 0.8149 (mp0) cc_final: 0.7835 (mp0) REVERT: B 306 ASP cc_start: 0.8607 (t0) cc_final: 0.8357 (t70) REVERT: B 478 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8056 (p) REVERT: B 532 SER cc_start: 0.8421 (p) cc_final: 0.8187 (p) REVERT: B 625 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 29 PHE cc_start: 0.8507 (t80) cc_final: 0.8138 (t80) REVERT: C 88 ASP cc_start: 0.8226 (m-30) cc_final: 0.7971 (m-30) REVERT: C 134 GLU cc_start: 0.8036 (mp0) cc_final: 0.7770 (mp0) REVERT: C 306 ASP cc_start: 0.8516 (t0) cc_final: 0.8179 (t70) REVERT: C 450 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8067 (mtpp) REVERT: C 514 TYR cc_start: 0.8029 (m-80) cc_final: 0.7756 (m-80) REVERT: C 533 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8145 (tp-100) REVERT: C 557 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.8028 (tt0) outliers start: 26 outliers final: 18 residues processed: 388 average time/residue: 0.6773 time to fit residues: 286.9969 Evaluate side-chains 391 residues out of total 1581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 369 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 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 350 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 243 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 C residue 96 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 557 GLU 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 186 optimal weight: 0.0050 chunk 126 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 163 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.0040 chunk 169 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.4406 ------------------------------------------------------------------------------- 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 = 0.3662 r_free = 0.3662 target = 0.121898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.106633 restraints weight = 21215.279| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.86 r_work: 0.3336 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15594 Z= 0.114 Angle : 0.542 13.066 21258 Z= 0.277 Chirality : 0.039 0.147 2370 Planarity : 0.004 0.040 2661 Dihedral : 3.934 24.102 2082 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.85 % Allowed : 19.48 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.20), residues: 1929 helix: 0.58 (0.15), residues: 1347 sheet: 0.44 (0.57), residues: 84 loop : -1.95 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 186 TYR 0.018 0.001 TYR B 621 PHE 0.034 0.001 PHE C 334 TRP 0.018 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00261 (15594) covalent geometry : angle 0.54153 (21258) hydrogen bonds : bond 0.04438 ( 718) hydrogen bonds : angle 3.61061 ( 2082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6728.93 seconds wall clock time: 115 minutes 1.11 seconds (6901.11 seconds total)