Starting phenix.real_space_refine on Fri Sep 27 05:57:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_39122.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_39122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_39122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_39122.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ybr_39122/09_2024/8ybr_39122.cif" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 9987 2.51 5 N 2472 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15150 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 5050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5050 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 9.31, per 1000 atoms: 0.61 Number of scatterers: 15150 At special positions: 0 Unit cell: (112.66, 115.24, 109.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2625 8.00 N 2472 7.00 C 9987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.39 Conformation dependent library (CDL) restraints added in 1.9 seconds 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3522 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 7 sheets defined 74.7% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 removed outlier: 4.088A pdb=" N PHE A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 25 " --> pdb=" O PHE A 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.761A pdb=" N LEU A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 75 removed outlier: 3.738A pdb=" N TYR A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 67 " --> pdb=" O MET A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.607A pdb=" N LYS A 80 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 103 removed outlier: 3.581A pdb=" N MET A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 115 through 124 removed outlier: 3.718A pdb=" N LEU A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.578A pdb=" N ALA A 136 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 168 removed outlier: 3.687A pdb=" N TRP A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 156 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER A 177 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 178 " --> pdb=" O LEU A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 178' Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.775A pdb=" N ASN A 188 " --> pdb=" O LYS A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 226 removed outlier: 3.817A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 203 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 216 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.957A pdb=" N GLN A 235 " --> pdb=" O THR A 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 304 removed outlier: 3.720A pdb=" N VAL A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.601A pdb=" N SER A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 3.987A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 380 removed outlier: 3.891A pdb=" N ALA A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.676A pdb=" N GLY A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 407 through 427 removed outlier: 3.747A pdb=" N ALA A 413 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 414 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 420 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL A 421 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 removed outlier: 3.567A pdb=" N VAL A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.514A pdb=" N VAL A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 460 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 463 " --> pdb=" O ALA A 459 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 removed outlier: 3.848A pdb=" N VAL A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 514 removed outlier: 4.077A pdb=" N ILE A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 508 " --> pdb=" O MET A 504 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 539 through 548 removed outlier: 3.556A pdb=" N VAL A 543 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 546 " --> pdb=" O GLU A 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 548 " --> pdb=" O TYR A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 removed outlier: 4.112A pdb=" N GLU A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.742A pdb=" N ALA A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 608 " --> pdb=" O SER A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 608' Processing helix chain 'A' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN A 647 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 36 removed outlier: 4.089A pdb=" N PHE B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 55 removed outlier: 3.763A pdb=" N LEU B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN B 53 " --> pdb=" O ASN B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 75 removed outlier: 3.739A pdb=" N TYR B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 67 " --> pdb=" O MET B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.608A pdb=" N LYS B 80 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 removed outlier: 3.582A pdb=" N MET B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.718A pdb=" N LEU B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 147 removed outlier: 3.577A pdb=" N ALA B 136 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 142 " --> pdb=" O GLN B 138 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 144 " --> pdb=" O MET B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 168 removed outlier: 3.688A pdb=" N TRP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 156 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER B 177 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 178 " --> pdb=" O LEU B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 178' Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.775A pdb=" N ASN B 188 " --> pdb=" O LYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 226 removed outlier: 3.819A pdb=" N ILE B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B 202 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 212 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.957A pdb=" N GLN B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA B 246 " --> pdb=" O MET B 242 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 304 removed outlier: 3.721A pdb=" N VAL B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.600A pdb=" N SER B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 3.988A pdb=" N LEU B 337 " --> pdb=" O PRO B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 380 removed outlier: 3.892A pdb=" N ALA B 374 " --> pdb=" O PHE B 370 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 3.677A pdb=" N GLY B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 407 through 427 removed outlier: 3.745A pdb=" N ALA B 413 " --> pdb=" O LYS B 409 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 420 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 421 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER B 426 " --> pdb=" O PHE B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 removed outlier: 3.569A pdb=" N VAL B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.514A pdb=" N VAL B 458 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 460 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 467 " --> pdb=" O ILE B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 484 removed outlier: 3.849A pdb=" N VAL B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 514 removed outlier: 4.077A pdb=" N ILE B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN B 507 " --> pdb=" O VAL B 503 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARG B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 528 through 533 Processing helix chain 'B' and resid 534 through 536 No H-bonds generated for 'chain 'B' and resid 534 through 536' Processing helix chain 'B' and resid 539 through 548 removed outlier: 3.554A pdb=" N VAL B 543 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 544 " --> pdb=" O ARG B 540 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE B 546 " --> pdb=" O GLU B 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 548 " --> pdb=" O TYR B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 removed outlier: 4.113A pdb=" N GLU B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 removed outlier: 3.742A pdb=" N ALA B 607 " --> pdb=" O PRO B 604 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 608 " --> pdb=" O SER B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 608' Processing helix chain 'B' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 36 removed outlier: 4.088A pdb=" N PHE C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 24 " --> pdb=" O TYR C 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE C 36 " --> pdb=" O ILE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 55 removed outlier: 3.762A pdb=" N LEU C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 53 " --> pdb=" O ASN C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 75 removed outlier: 3.738A pdb=" N TYR C 59 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 67 " --> pdb=" O MET C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.608A pdb=" N LYS C 80 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.580A pdb=" N MET C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.719A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.578A pdb=" N ALA C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 140 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 142 " --> pdb=" O GLN C 138 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 168 removed outlier: 3.687A pdb=" N TRP C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.794A pdb=" N SER C 177 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 178 " --> pdb=" O LEU C 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 174 through 178' Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.774A pdb=" N ASN C 188 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.742A pdb=" N VAL C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 226 removed outlier: 3.819A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 202 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C 203 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 216 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.958A pdb=" N GLN C 235 " --> pdb=" O THR C 231 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA C 246 " --> pdb=" O MET C 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 279 removed outlier: 3.825A pdb=" N MET C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C 270 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 304 removed outlier: 3.721A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.600A pdb=" N SER C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.608A pdb=" N TYR C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Proline residue: C 333 - end of helix removed outlier: 3.986A pdb=" N LEU C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.532A pdb=" N GLY C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 380 removed outlier: 3.891A pdb=" N ALA C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 removed outlier: 3.677A pdb=" N GLY C 387 " --> pdb=" O MET C 383 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 407 through 427 removed outlier: 3.746A pdb=" N ALA C 413 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 420 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 421 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 437 removed outlier: 3.568A pdb=" N VAL C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.513A pdb=" N VAL C 458 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 460 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 463 " --> pdb=" O ALA C 459 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 467 " --> pdb=" O ILE C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 484 removed outlier: 3.848A pdb=" N VAL C 480 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 481 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 514 removed outlier: 4.076A pdb=" N ILE C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 492 " --> pdb=" O SER C 488 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG C 508 " --> pdb=" O MET C 504 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C 509 " --> pdb=" O GLU C 505 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 512 " --> pdb=" O ARG C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 528 through 533 Processing helix chain 'C' and resid 534 through 536 No H-bonds generated for 'chain 'C' and resid 534 through 536' Processing helix chain 'C' and resid 539 through 548 removed outlier: 3.556A pdb=" N VAL C 543 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 546 " --> pdb=" O GLU C 542 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 548 " --> pdb=" O TYR C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 564 removed outlier: 4.113A pdb=" N GLU C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL C 561 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 608 removed outlier: 3.743A pdb=" N ALA C 607 " --> pdb=" O PRO C 604 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 608 " --> pdb=" O SER C 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 604 through 608' Processing helix chain 'C' and resid 641 through 664 removed outlier: 3.518A pdb=" N ASN C 647 " --> pdb=" O GLU C 643 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 651 " --> pdb=" O ASN C 647 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 655 " --> pdb=" O ASP C 651 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 662 " --> pdb=" O GLN C 658 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.593A pdb=" N ARG A 13 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 580 through 582 removed outlier: 3.518A pdb=" N VAL A 596 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.594A pdb=" N ARG B 13 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 568 through 569 removed outlier: 4.868A pdb=" N ASN B 568 " --> pdb=" O GLY B 585 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 580 through 582 removed outlier: 3.516A pdb=" N VAL B 596 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 13 through 14 removed outlier: 3.594A pdb=" N ARG C 13 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 580 through 582 removed outlier: 3.518A pdb=" N VAL C 596 " --> pdb=" O VAL C 580 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 4.02 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: 0.00 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.260 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15594 Z= 0.317 Angle : 0.674 9.309 21258 Z= 0.384 Chirality : 0.043 0.136 2370 Planarity : 0.005 0.046 2661 Dihedral : 12.453 88.814 5325 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.70 % Allowed : 4.47 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.55 (0.15), residues: 1929 helix: -2.78 (0.11), residues: 1308 sheet: -2.88 (0.50), residues: 90 loop : -3.05 (0.22), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 327 HIS 0.006 0.001 HIS B 217 PHE 0.013 0.001 PHE B 334 TYR 0.008 0.001 TYR C 640 ARG 0.008 0.001 ARG C 619 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 391 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.7706 (tpt) cc_final: 0.6807 (tpt) REVERT: A 440 LYS cc_start: 0.8339 (ttpt) cc_final: 0.8078 (ttpt) REVERT: A 529 GLN cc_start: 0.7860 (mp10) cc_final: 0.7510 (mp10) REVERT: A 556 ASP cc_start: 0.7398 (p0) cc_final: 0.7028 (p0) REVERT: A 629 SER cc_start: 0.7839 (m) cc_final: 0.7398 (t) REVERT: B 60 MET cc_start: 0.7990 (mmm) cc_final: 0.7406 (mmt) REVERT: B 94 TYR cc_start: 0.7301 (t80) cc_final: 0.7055 (t80) REVERT: B 134 GLU cc_start: 0.7163 (mp0) cc_final: 0.6960 (mp0) REVERT: B 263 ASP cc_start: 0.6785 (m-30) cc_final: 0.6520 (m-30) REVERT: B 529 GLN cc_start: 0.7758 (mp10) cc_final: 0.7481 (mp10) REVERT: B 625 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7419 (mm-30) REVERT: C 29 PHE cc_start: 0.8132 (t80) cc_final: 0.7752 (t80) REVERT: C 230 HIS cc_start: 0.8298 (m-70) cc_final: 0.8097 (m-70) REVERT: C 440 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8074 (ttpt) REVERT: C 655 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7579 (ttm-80) outliers start: 11 outliers final: 4 residues processed: 394 average time/residue: 1.3604 time to fit residues: 584.9506 Evaluate side-chains 359 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 355 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 634 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 chunk 150 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.4980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 372 ASN A 509 GLN A 644 GLN A 647 ASN B 372 ASN B 509 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN C 49 ASN C 372 ASN C 509 GLN C 595 GLN C 647 ASN C 658 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15594 Z= 0.197 Angle : 0.559 5.539 21258 Z= 0.297 Chirality : 0.039 0.131 2370 Planarity : 0.005 0.056 2661 Dihedral : 4.737 30.489 2091 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.17 % Allowed : 12.77 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.17), residues: 1929 helix: -1.72 (0.13), residues: 1341 sheet: -2.18 (0.48), residues: 90 loop : -2.54 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 661 PHE 0.016 0.001 PHE C 334 TYR 0.021 0.001 TYR C 621 ARG 0.008 0.001 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 373 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 263 ASP cc_start: 0.6591 (m-30) cc_final: 0.6340 (m-30) REVERT: A 529 GLN cc_start: 0.7932 (mp10) cc_final: 0.7699 (mp10) REVERT: A 621 TYR cc_start: 0.7948 (p90) cc_final: 0.7585 (p90) REVERT: B 60 MET cc_start: 0.8015 (mmm) cc_final: 0.7367 (mmt) REVERT: B 108 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7165 (mt) REVERT: B 259 ARG cc_start: 0.7030 (tpt-90) cc_final: 0.6718 (tmt-80) REVERT: B 558 VAL cc_start: 0.7660 (p) cc_final: 0.7423 (p) REVERT: C 440 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7897 (ttpt) REVERT: C 514 TYR cc_start: 0.7457 (m-80) cc_final: 0.7103 (m-80) REVERT: C 533 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7761 (tp-100) REVERT: C 621 TYR cc_start: 0.8040 (p90) cc_final: 0.7726 (p90) REVERT: C 655 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7466 (ttm110) outliers start: 34 outliers final: 15 residues processed: 386 average time/residue: 1.2429 time to fit residues: 526.3722 Evaluate side-chains 367 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 351 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 118 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 658 GLN B 533 GLN B 627 HIS C 49 ASN C 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2334 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= 0.190 Angle : 0.517 5.650 21258 Z= 0.273 Chirality : 0.039 0.135 2370 Planarity : 0.004 0.042 2661 Dihedral : 4.288 25.745 2082 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.75 % Allowed : 14.05 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.18), residues: 1929 helix: -0.97 (0.14), residues: 1341 sheet: -1.26 (0.51), residues: 84 loop : -2.23 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.021 0.001 PHE B 25 TYR 0.022 0.001 TYR B 621 ARG 0.009 0.001 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 360 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ILE cc_start: 0.8220 (pt) cc_final: 0.7970 (mt) REVERT: A 108 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6989 (mt) REVERT: A 263 ASP cc_start: 0.6519 (m-30) cc_final: 0.6278 (m-30) REVERT: A 529 GLN cc_start: 0.7926 (mp10) cc_final: 0.7725 (mp10) REVERT: A 533 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7831 (tm130) REVERT: A 542 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6937 (tm-30) REVERT: A 621 TYR cc_start: 0.8142 (p90) cc_final: 0.7846 (p90) REVERT: B 32 ILE cc_start: 0.8287 (pt) cc_final: 0.8028 (mt) REVERT: B 108 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7101 (mt) REVERT: C 32 ILE cc_start: 0.8420 (pt) cc_final: 0.8072 (mt) REVERT: C 514 TYR cc_start: 0.7460 (m-80) cc_final: 0.7137 (m-80) REVERT: C 533 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7701 (tp-100) outliers start: 43 outliers final: 24 residues processed: 376 average time/residue: 1.3517 time to fit residues: 557.5229 Evaluate side-chains 385 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 358 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ILE 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 437 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 533 GLN Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 500 LYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.5980 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 175 optimal weight: 0.0770 chunk 185 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 647 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15594 Z= 0.186 Angle : 0.514 9.470 21258 Z= 0.271 Chirality : 0.039 0.142 2370 Planarity : 0.004 0.044 2661 Dihedral : 4.165 25.249 2082 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.49 % Allowed : 14.94 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.19), residues: 1929 helix: -0.57 (0.14), residues: 1341 sheet: -0.86 (0.52), residues: 84 loop : -2.11 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.020 0.001 PHE C 334 TYR 0.020 0.001 TYR B 621 ARG 0.006 0.000 ARG A 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 366 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7909 (m-30) cc_final: 0.7582 (m-30) REVERT: A 263 ASP cc_start: 0.6562 (m-30) cc_final: 0.6298 (m-30) REVERT: A 334 PHE cc_start: 0.7931 (t80) cc_final: 0.7130 (t80) REVERT: A 533 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7802 (tm130) REVERT: A 542 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7088 (tm-30) REVERT: A 621 TYR cc_start: 0.8214 (p90) cc_final: 0.7893 (p90) REVERT: B 108 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7088 (mt) REVERT: B 508 ARG cc_start: 0.6599 (ttp80) cc_final: 0.6291 (ttp80) REVERT: B 533 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7705 (tp-100) REVERT: B 621 TYR cc_start: 0.7942 (p90) cc_final: 0.7668 (p90) REVERT: C 32 ILE cc_start: 0.8385 (pt) cc_final: 0.8145 (mt) REVERT: C 331 TRP cc_start: 0.8459 (m100) cc_final: 0.8210 (m100) REVERT: C 514 TYR cc_start: 0.7474 (m-80) cc_final: 0.7169 (m-80) REVERT: C 529 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7794 (pp30) REVERT: C 533 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7702 (tp-100) REVERT: C 542 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7052 (tm-30) REVERT: C 557 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7704 (tt0) outliers start: 39 outliers final: 21 residues processed: 380 average time/residue: 1.2357 time to fit residues: 514.8626 Evaluate side-chains 385 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 359 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET 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 397 THR 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 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 B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 325 TRP Chi-restraints excluded: chain C residue 334 PHE Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 557 GLU Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 595 GLN C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15594 Z= 0.249 Angle : 0.547 8.805 21258 Z= 0.287 Chirality : 0.041 0.140 2370 Planarity : 0.004 0.044 2661 Dihedral : 4.197 25.611 2082 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.68 % Allowed : 15.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1929 helix: -0.35 (0.14), residues: 1338 sheet: -0.75 (0.53), residues: 84 loop : -2.12 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.005 0.001 HIS A 217 PHE 0.026 0.001 PHE B 25 TYR 0.019 0.001 TYR B 621 ARG 0.006 0.000 ARG B 655 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 374 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7897 (m-30) cc_final: 0.7561 (m-30) REVERT: A 263 ASP cc_start: 0.6523 (m-30) cc_final: 0.6263 (m-30) REVERT: A 334 PHE cc_start: 0.7858 (t80) cc_final: 0.7097 (t80) REVERT: A 533 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7582 (tp-100) REVERT: A 542 GLU cc_start: 0.7441 (tm-30) cc_final: 0.7128 (tm-30) REVERT: A 557 GLU cc_start: 0.8258 (tm-30) cc_final: 0.8036 (tt0) REVERT: B 24 SER cc_start: 0.8282 (p) cc_final: 0.8075 (m) REVERT: B 108 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7016 (mt) REVERT: B 508 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6294 (ttp80) REVERT: B 557 GLU cc_start: 0.8290 (tt0) cc_final: 0.8028 (tt0) REVERT: C 88 ASP cc_start: 0.7978 (m-30) cc_final: 0.7728 (m-30) REVERT: C 306 ASP cc_start: 0.7940 (t0) cc_final: 0.7648 (t70) REVERT: C 440 LYS cc_start: 0.8349 (ttpt) cc_final: 0.8021 (ttpp) REVERT: C 514 TYR cc_start: 0.7503 (m-80) cc_final: 0.7124 (m-80) REVERT: C 533 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7665 (tp-100) REVERT: C 557 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7726 (tt0) outliers start: 42 outliers final: 21 residues processed: 392 average time/residue: 1.2597 time to fit residues: 541.1147 Evaluate side-chains 391 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 367 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 397 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 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 62 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 185 optimal weight: 0.7980 chunk 154 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 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 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15594 Z= 0.251 Angle : 0.556 9.582 21258 Z= 0.291 Chirality : 0.041 0.140 2370 Planarity : 0.004 0.043 2661 Dihedral : 4.185 24.967 2082 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.81 % Allowed : 16.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1929 helix: -0.18 (0.14), residues: 1350 sheet: -0.61 (0.52), residues: 84 loop : -2.08 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 327 HIS 0.005 0.001 HIS A 217 PHE 0.023 0.001 PHE C 25 TYR 0.019 0.001 TYR B 621 ARG 0.007 0.000 ARG A 186 *********************** 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 428 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 384 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8390 (p) cc_final: 0.8114 (m) REVERT: A 263 ASP cc_start: 0.6521 (m-30) cc_final: 0.6260 (m-30) REVERT: A 533 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7572 (tp-100) REVERT: A 542 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7136 (tm-30) REVERT: A 583 GLU cc_start: 0.7351 (tt0) cc_final: 0.7094 (tp30) REVERT: A 593 ILE cc_start: 0.8557 (mm) cc_final: 0.8294 (mm) REVERT: B 88 ASP cc_start: 0.7999 (m-30) cc_final: 0.7692 (m-30) REVERT: B 108 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7004 (mt) REVERT: B 306 ASP cc_start: 0.7994 (t0) cc_final: 0.7753 (t70) REVERT: B 508 ARG cc_start: 0.6598 (ttp80) cc_final: 0.6265 (ttp80) REVERT: C 29 PHE cc_start: 0.8436 (t80) cc_final: 0.8083 (t80) REVERT: C 61 MET cc_start: 0.7176 (mmp) cc_final: 0.6836 (mmp) REVERT: C 88 ASP cc_start: 0.7950 (m-30) cc_final: 0.7652 (m-30) REVERT: C 306 ASP cc_start: 0.7923 (t0) cc_final: 0.7643 (t70) REVERT: C 331 TRP cc_start: 0.8474 (m100) cc_final: 0.8247 (m100) REVERT: C 440 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7994 (ttpp) REVERT: C 514 TYR cc_start: 0.7507 (m-80) cc_final: 0.7111 (m-80) REVERT: C 533 GLN cc_start: 0.8159 (tm-30) cc_final: 0.7650 (tp-100) REVERT: C 557 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: C 619 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7534 (mmm160) outliers start: 44 outliers final: 24 residues processed: 405 average time/residue: 1.2475 time to fit residues: 555.3478 Evaluate side-chains 391 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 364 time to evaluate : 1.610 ------------------------------------------------------------------------------- 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 397 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 589 GLU Chi-restraints excluded: chain B residue 643 GLU Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 96 SER 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 565 LYS Chi-restraints excluded: chain C residue 643 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 115 optimal weight: 0.4980 chunk 112 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 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 ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 GLN C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15594 Z= 0.208 Angle : 0.553 11.123 21258 Z= 0.286 Chirality : 0.040 0.145 2370 Planarity : 0.004 0.042 2661 Dihedral : 4.110 25.039 2082 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.30 % Allowed : 17.62 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1929 helix: 0.02 (0.14), residues: 1350 sheet: -0.44 (0.52), residues: 84 loop : -2.03 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.023 0.001 PHE A 334 TYR 0.019 0.001 TYR B 621 ARG 0.009 0.000 ARG A 186 *********************** 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 401 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 365 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8390 (p) cc_final: 0.8119 (m) REVERT: A 263 ASP cc_start: 0.6515 (m-30) cc_final: 0.6257 (m-30) REVERT: A 508 ARG cc_start: 0.6881 (ttp80) cc_final: 0.6573 (ttp80) REVERT: A 529 GLN cc_start: 0.7989 (pm20) cc_final: 0.7654 (mp10) REVERT: A 533 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7567 (tp-100) REVERT: A 557 GLU cc_start: 0.8140 (tt0) cc_final: 0.7901 (tt0) REVERT: A 583 GLU cc_start: 0.7357 (tt0) cc_final: 0.7028 (tp30) REVERT: A 593 ILE cc_start: 0.8566 (mm) cc_final: 0.8331 (mm) REVERT: B 24 SER cc_start: 0.8264 (p) cc_final: 0.8054 (m) REVERT: B 108 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6993 (mt) REVERT: C 29 PHE cc_start: 0.8437 (t80) cc_final: 0.8060 (t80) REVERT: C 61 MET cc_start: 0.7185 (mmp) cc_final: 0.6876 (mmp) REVERT: C 134 GLU cc_start: 0.7013 (mp0) cc_final: 0.6791 (mp0) REVERT: C 331 TRP cc_start: 0.8460 (m100) cc_final: 0.8246 (m100) REVERT: C 514 TYR cc_start: 0.7498 (m-80) cc_final: 0.7147 (m-80) REVERT: C 533 GLN cc_start: 0.8156 (tm-30) cc_final: 0.7640 (tp-100) REVERT: C 557 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: C 619 ARG cc_start: 0.7715 (mmm-85) cc_final: 0.7471 (mmm160) outliers start: 36 outliers final: 23 residues processed: 381 average time/residue: 1.2892 time to fit residues: 537.4760 Evaluate side-chains 391 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 365 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 243 MET 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 516 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 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 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 73 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15594 Z= 0.222 Angle : 0.556 11.936 21258 Z= 0.288 Chirality : 0.040 0.152 2370 Planarity : 0.004 0.041 2661 Dihedral : 4.075 24.675 2082 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.36 % Allowed : 17.75 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1929 helix: 0.18 (0.15), residues: 1350 sheet: -0.25 (0.52), residues: 84 loop : -2.00 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.029 0.001 PHE C 25 TYR 0.018 0.001 TYR B 621 ARG 0.008 0.000 ARG A 186 *********************** 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 403 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 366 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8391 (p) cc_final: 0.8121 (m) REVERT: A 96 SER cc_start: 0.8379 (m) cc_final: 0.8109 (p) REVERT: A 263 ASP cc_start: 0.6520 (m-30) cc_final: 0.6236 (m-30) REVERT: A 508 ARG cc_start: 0.6886 (ttp80) cc_final: 0.6597 (ttp80) REVERT: A 529 GLN cc_start: 0.8001 (pm20) cc_final: 0.7654 (mp10) REVERT: A 533 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7568 (tp-100) REVERT: A 557 GLU cc_start: 0.8134 (tt0) cc_final: 0.7912 (tt0) REVERT: A 583 GLU cc_start: 0.7341 (tt0) cc_final: 0.7090 (tt0) REVERT: B 24 SER cc_start: 0.8250 (p) cc_final: 0.8043 (m) REVERT: B 108 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6990 (mt) REVERT: B 542 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6680 (tm-30) REVERT: C 29 PHE cc_start: 0.8440 (t80) cc_final: 0.8053 (t80) REVERT: C 331 TRP cc_start: 0.8465 (m100) cc_final: 0.8247 (m100) REVERT: C 514 TYR cc_start: 0.7504 (m-80) cc_final: 0.7137 (m-80) REVERT: C 533 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7631 (tp-100) REVERT: C 557 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: C 619 ARG cc_start: 0.7719 (mmm-85) cc_final: 0.7480 (mmm160) outliers start: 37 outliers final: 24 residues processed: 384 average time/residue: 1.2591 time to fit residues: 530.0323 Evaluate side-chains 392 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 365 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 506 SER Chi-restraints excluded: chain B residue 512 GLN Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 634 ASP Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.0020 chunk 161 optimal weight: 0.8980 chunk 172 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 0.4980 chunk 163 optimal weight: 0.6980 chunk 171 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN C 283 GLN ** C 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15594 Z= 0.160 Angle : 0.540 12.377 21258 Z= 0.276 Chirality : 0.038 0.145 2370 Planarity : 0.004 0.040 2661 Dihedral : 3.940 24.449 2082 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.79 % Allowed : 18.52 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.19), residues: 1929 helix: 0.41 (0.15), residues: 1350 sheet: 0.04 (0.54), residues: 84 loop : -1.98 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 PHE 0.023 0.001 PHE B 334 TYR 0.017 0.001 TYR B 621 ARG 0.008 0.000 ARG A 186 *********************** 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 397 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 369 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8403 (p) cc_final: 0.8136 (m) REVERT: A 325 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.7163 (m100) REVERT: A 508 ARG cc_start: 0.6822 (ttp80) cc_final: 0.6543 (ttp80) REVERT: A 529 GLN cc_start: 0.8014 (pm20) cc_final: 0.7684 (mp10) REVERT: A 533 GLN cc_start: 0.8046 (tm130) cc_final: 0.7644 (tp-100) REVERT: A 557 GLU cc_start: 0.8127 (tt0) cc_final: 0.7916 (tt0) REVERT: B 108 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6983 (mt) REVERT: B 325 TRP cc_start: 0.8257 (OUTLIER) cc_final: 0.7318 (m100) REVERT: C 29 PHE cc_start: 0.8438 (t80) cc_final: 0.8048 (t80) REVERT: C 331 TRP cc_start: 0.8445 (m100) cc_final: 0.8201 (m100) REVERT: C 450 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7779 (mtmm) REVERT: C 514 TYR cc_start: 0.7470 (m-80) cc_final: 0.7196 (m-10) REVERT: C 533 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7633 (tp-100) REVERT: C 557 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7710 (tt0) REVERT: C 619 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.7428 (mmm160) outliers start: 28 outliers final: 10 residues processed: 381 average time/residue: 1.2992 time to fit residues: 542.5726 Evaluate side-chains 380 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 366 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 512 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 512 GLN Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 500 LYS 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 182 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.0670 chunk 120 optimal weight: 0.0040 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN C 49 ASN C 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3293 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= 0.171 Angle : 0.543 13.251 21258 Z= 0.278 Chirality : 0.039 0.140 2370 Planarity : 0.004 0.040 2661 Dihedral : 3.880 24.166 2082 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.21 % Allowed : 19.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1929 helix: 0.55 (0.15), residues: 1350 sheet: 0.25 (0.55), residues: 84 loop : -1.88 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.003 0.001 HIS A 217 PHE 0.027 0.001 PHE C 25 TYR 0.019 0.001 TYR B 621 ARG 0.010 0.000 ARG A 186 ********************** 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 391 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 372 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8400 (p) cc_final: 0.8137 (m) REVERT: A 325 TRP cc_start: 0.8004 (OUTLIER) cc_final: 0.7220 (m100) REVERT: A 508 ARG cc_start: 0.6834 (ttp80) cc_final: 0.6564 (ttp80) REVERT: A 529 GLN cc_start: 0.8019 (pm20) cc_final: 0.7686 (mp10) REVERT: A 533 GLN cc_start: 0.8042 (tm130) cc_final: 0.7662 (tp-100) REVERT: A 557 GLU cc_start: 0.8112 (tt0) cc_final: 0.7911 (tt0) REVERT: A 583 GLU cc_start: 0.7291 (tt0) cc_final: 0.6942 (tp30) REVERT: B 108 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6985 (mt) REVERT: C 29 PHE cc_start: 0.8457 (t80) cc_final: 0.8123 (t80) REVERT: C 88 ASP cc_start: 0.7990 (m-30) cc_final: 0.7669 (m-30) REVERT: C 306 ASP cc_start: 0.7904 (t0) cc_final: 0.7624 (t70) REVERT: C 331 TRP cc_start: 0.8444 (m100) cc_final: 0.8196 (m100) REVERT: C 450 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7711 (mtpp) REVERT: C 514 TYR cc_start: 0.7464 (m-80) cc_final: 0.7191 (m-10) REVERT: C 533 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7605 (tp-100) REVERT: C 557 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: C 619 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7430 (mmm160) outliers start: 19 outliers final: 11 residues processed: 381 average time/residue: 1.3205 time to fit residues: 551.0575 Evaluate side-chains 375 residues out of total 1581 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 361 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 325 TRP Chi-restraints excluded: chain A residue 512 GLN Chi-restraints excluded: chain A residue 589 GLU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 325 TRP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 512 GLN 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 162 optimal weight: 0.0470 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 156 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.121163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105890 restraints weight = 21215.824| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.87 r_work: 0.3323 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3332 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= 0.198 Angle : 0.559 13.171 21258 Z= 0.285 Chirality : 0.040 0.144 2370 Planarity : 0.004 0.042 2661 Dihedral : 3.909 24.187 2082 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.28 % Allowed : 19.03 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.20), residues: 1929 helix: 0.63 (0.15), residues: 1341 sheet: 0.37 (0.55), residues: 84 loop : -1.90 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 327 HIS 0.004 0.001 HIS A 217 PHE 0.024 0.001 PHE B 334 TYR 0.020 0.001 TYR B 621 ARG 0.010 0.000 ARG A 186 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7924.31 seconds wall clock time: 137 minutes 40.92 seconds (8260.92 seconds total)