Starting phenix.real_space_refine on Mon Jul 28 03:21:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.map" model { file = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vwc_32152/07_2025/7vwc_32152.cif" } resolution = 3.53 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= -0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 46 5.16 5 C 6340 2.51 5 N 1741 2.21 5 O 1763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4929 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 21, 'TRANS': 595} Chain breaks: 2 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 21, 'TRANS': 590} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'82T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.63, per 1000 atoms: 0.57 Number of scatterers: 9892 At special positions: 0 Unit cell: (103.88, 147.34, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 P 2 15.00 O 1763 8.00 N 1741 7.00 C 6340 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 7 sheets defined 61.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 68 through 83 removed outlier: 3.698A pdb=" N LEU A 72 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.753A pdb=" N VAL A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 124 removed outlier: 3.774A pdb=" N CYS A 121 " --> pdb=" O ARG A 117 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 3.705A pdb=" N GLN A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 136 " --> pdb=" O TRP A 132 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 147 removed outlier: 3.981A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 175 removed outlier: 3.685A pdb=" N ARG A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 217 removed outlier: 3.604A pdb=" N PHE A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 235 removed outlier: 3.762A pdb=" N ALA A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N TYR A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 4.077A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.681A pdb=" N ARG A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 279 " --> pdb=" O ARG A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 298 through 308 removed outlier: 3.831A pdb=" N GLU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.811A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 344 through 354 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 374 through 380 removed outlier: 3.744A pdb=" N SER A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 407 through 430 removed outlier: 3.591A pdb=" N GLU A 411 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 418 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 4.127A pdb=" N PHE A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.698A pdb=" N VAL A 557 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.912A pdb=" N GLN A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 585 through 589 removed outlier: 3.771A pdb=" N ILE A 588 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 589 " --> pdb=" O HIS A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 585 through 589' Processing helix chain 'A' and resid 600 through 604 Processing helix chain 'A' and resid 606 through 622 removed outlier: 3.684A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A 612 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 618 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.764A pdb=" N GLU A 640 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 645 " --> pdb=" O GLY A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.845A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 666 " --> pdb=" O LEU A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 700 removed outlier: 3.962A pdb=" N GLN A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.539A pdb=" N CYS A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 83 removed outlier: 3.684A pdb=" N LEU B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 81 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.555A pdb=" N VAL B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 135 removed outlier: 3.578A pdb=" N TRP B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.517A pdb=" N ALA B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.538A pdb=" N PHE B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.114A pdb=" N SER B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.734A pdb=" N ALA B 209 " --> pdb=" O ALA B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.633A pdb=" N ASP B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 4.058A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 270 removed outlier: 3.771A pdb=" N PHE B 265 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.614A pdb=" N MET B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.589A pdb=" N VAL B 287 " --> pdb=" O HIS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.618A pdb=" N PHE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 312 removed outlier: 3.768A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 321 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.864A pdb=" N PHE B 333 " --> pdb=" O MET B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 410 through 429 removed outlier: 4.233A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 423 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 514 through 521 removed outlier: 3.878A pdb=" N ARG B 518 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 552 through 557 removed outlier: 3.768A pdb=" N VAL B 557 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 570 Processing helix chain 'B' and resid 575 through 583 removed outlier: 3.687A pdb=" N VAL B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 606 through 622 removed outlier: 3.721A pdb=" N GLY B 614 " --> pdb=" O LYS B 610 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 618 " --> pdb=" O GLY B 614 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 619 " --> pdb=" O MET B 615 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B 621 " --> pdb=" O ARG B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 651 removed outlier: 3.778A pdb=" N GLY B 641 " --> pdb=" O ILE B 637 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 664 removed outlier: 3.652A pdb=" N LEU B 663 " --> pdb=" O ARG B 660 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP B 664 " --> pdb=" O PRO B 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 660 through 664' Processing helix chain 'B' and resid 685 through 690 removed outlier: 3.506A pdb=" N LEU B 690 " --> pdb=" O SER B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 702 removed outlier: 3.919A pdb=" N ARG B 698 " --> pdb=" O GLU B 694 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 700 " --> pdb=" O LYS B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 713 removed outlier: 3.631A pdb=" N MET B 709 " --> pdb=" O GLY B 705 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing sheet with id=AA1, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.652A pdb=" N VAL A 530 " --> pdb=" O GLU A 477 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 482 removed outlier: 6.860A pdb=" N ILE A 481 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 506 removed outlier: 6.790A pdb=" N LEU A 504 " --> pdb=" O LEU A 671 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AA5, first strand: chain 'B' and resid 467 through 469 removed outlier: 3.723A pdb=" N LYS B 533 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 506 removed outlier: 3.632A pdb=" N PHE B 673 " --> pdb=" O THR B 506 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.476A pdb=" N PHE B 540 " --> pdb=" O LEU B 627 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1578 1.31 - 1.43: 2725 1.43 - 1.56: 5711 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 10094 Sorted by residual: bond pdb=" C18 82T B 801 " pdb=" O20 82T B 801 " ideal model delta sigma weight residual 1.335 1.399 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C18 82T A 801 " pdb=" O20 82T A 801 " ideal model delta sigma weight residual 1.335 1.395 -0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" N TYR B 406 " pdb=" CA TYR B 406 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.31e-02 5.83e+03 5.14e+00 bond pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.33e-02 5.65e+03 5.03e+00 bond pdb=" N THR B 693 " pdb=" CA THR B 693 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.35e-02 5.49e+03 4.37e+00 ... (remaining 10089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 13365 2.67 - 5.33: 240 5.33 - 8.00: 27 8.00 - 10.66: 8 10.66 - 13.33: 5 Bond angle restraints: 13645 Sorted by residual: angle pdb=" N TYR B 406 " pdb=" CA TYR B 406 " pdb=" C TYR B 406 " ideal model delta sigma weight residual 114.31 105.53 8.78 1.29e+00 6.01e-01 4.63e+01 angle pdb=" N ILE B 399 " pdb=" CA ILE B 399 " pdb=" C ILE B 399 " ideal model delta sigma weight residual 112.96 106.89 6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA GLU A 471 " pdb=" C GLU A 471 " pdb=" O GLU A 471 " ideal model delta sigma weight residual 121.54 116.16 5.38 1.16e+00 7.43e-01 2.15e+01 angle pdb=" N THR B 693 " pdb=" CA THR B 693 " pdb=" C THR B 693 " ideal model delta sigma weight residual 113.43 107.67 5.76 1.26e+00 6.30e-01 2.09e+01 angle pdb=" O24 82T A 801 " pdb=" P25 82T A 801 " pdb=" O28 82T A 801 " ideal model delta sigma weight residual 97.38 110.71 -13.33 3.00e+00 1.11e-01 1.97e+01 ... (remaining 13640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.42: 5817 29.42 - 58.83: 239 58.83 - 88.25: 32 88.25 - 117.66: 2 117.66 - 147.08: 1 Dihedral angle restraints: 6091 sinusoidal: 2516 harmonic: 3575 Sorted by residual: dihedral pdb=" CA GLU A 682 " pdb=" C GLU A 682 " pdb=" N LYS A 683 " pdb=" CA LYS A 683 " ideal model delta harmonic sigma weight residual -180.00 -151.70 -28.30 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA GLU B 271 " pdb=" C GLU B 271 " pdb=" N GLU B 272 " pdb=" CA GLU B 272 " ideal model delta harmonic sigma weight residual 180.00 154.16 25.84 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU B 690 " pdb=" C LEU B 690 " pdb=" N SER B 691 " pdb=" CA SER B 691 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 962 0.047 - 0.093: 453 0.093 - 0.140: 100 0.140 - 0.186: 5 0.186 - 0.233: 3 Chirality restraints: 1523 Sorted by residual: chirality pdb=" CA GLU A 471 " pdb=" N GLU A 471 " pdb=" C GLU A 471 " pdb=" CB GLU A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL B 347 " pdb=" CA VAL B 347 " pdb=" CG1 VAL B 347 " pdb=" CG2 VAL B 347 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE B 558 " pdb=" CA ILE B 558 " pdb=" CG1 ILE B 558 " pdb=" CG2 ILE B 558 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1520 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 236 " 0.030 2.00e-02 2.50e+03 6.28e-02 3.94e+01 pdb=" C ARG A 236 " -0.108 2.00e-02 2.50e+03 pdb=" O ARG A 236 " 0.042 2.00e-02 2.50e+03 pdb=" N GLY A 237 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 545 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO B 546 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 546 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 546 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 242 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 243 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.024 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 257 2.68 - 3.24: 9808 3.24 - 3.79: 14241 3.79 - 4.35: 20304 4.35 - 4.90: 32289 Nonbonded interactions: 76899 Sorted by model distance: nonbonded pdb=" O ASN B 318 " pdb=" ND2 ASN B 318 " model vdw 2.127 3.120 nonbonded pdb=" OG SER B 562 " pdb=" OD1 ASP B 565 " model vdw 2.218 3.040 nonbonded pdb=" NH2 ARG A 189 " pdb=" OD2 ASP A 428 " model vdw 2.230 3.120 nonbonded pdb=" NE2 GLN B 611 " pdb=" O CYS B 631 " model vdw 2.246 3.120 nonbonded pdb=" O GLU B 471 " pdb=" NZ LYS B 624 " model vdw 2.257 3.120 ... (remaining 76894 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' and (resid 68 through 720 or resid 801)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.090 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 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 : 0.009 0.069 10094 Z= 0.372 Angle : 0.933 13.330 13645 Z= 0.502 Chirality : 0.052 0.233 1523 Planarity : 0.005 0.063 1728 Dihedral : 16.123 147.075 3787 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 0.38 % Allowed : 1.06 % Favored : 98.56 % 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: -4.78 (0.21), residues: 1217 helix: -3.47 (0.14), residues: 795 sheet: -2.35 (0.74), residues: 47 loop : -1.96 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 326 HIS 0.006 0.002 HIS B 97 PHE 0.018 0.002 PHE B 162 TYR 0.018 0.002 TYR B 174 ARG 0.008 0.001 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.29371 ( 356) hydrogen bonds : angle 10.40196 ( 1020) covalent geometry : bond 0.00858 (10094) covalent geometry : angle 0.93326 (13645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 427 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7510 (mt-10) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.2369 time to fit residues: 46.2311 Evaluate side-chains 121 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 95 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110640 restraints weight = 13466.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108115 restraints weight = 10882.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109582 restraints weight = 10628.196| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10094 Z= 0.128 Angle : 0.664 10.215 13645 Z= 0.335 Chirality : 0.042 0.164 1523 Planarity : 0.004 0.060 1728 Dihedral : 8.638 119.335 1438 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 0.29 % Allowed : 7.88 % Favored : 91.83 % 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: -4.05 (0.22), residues: 1217 helix: -2.84 (0.16), residues: 785 sheet: -2.21 (0.69), residues: 57 loop : -1.85 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 242 HIS 0.004 0.001 HIS A 667 PHE 0.015 0.001 PHE A 673 TYR 0.013 0.001 TYR B 310 ARG 0.005 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 356) hydrogen bonds : angle 5.94420 ( 1020) covalent geometry : bond 0.00278 (10094) covalent geometry : angle 0.66430 (13645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 157 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8743 (pt) cc_final: 0.8376 (mt) REVERT: A 411 GLU cc_start: 0.6740 (tt0) cc_final: 0.6474 (mt-10) REVERT: A 427 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7234 (mt-10) REVERT: A 598 MET cc_start: 0.7162 (mtt) cc_final: 0.6927 (mtp) REVERT: B 329 MET cc_start: 0.8641 (tmm) cc_final: 0.8376 (tmm) REVERT: B 545 ARG cc_start: 0.7592 (ptt90) cc_final: 0.7379 (ptt-90) outliers start: 3 outliers final: 2 residues processed: 159 average time/residue: 0.2317 time to fit residues: 51.1664 Evaluate side-chains 129 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 20.0000 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 556 GLN B 318 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114609 restraints weight = 13454.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.112741 restraints weight = 11504.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114164 restraints weight = 10954.313| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10094 Z= 0.124 Angle : 0.592 10.122 13645 Z= 0.301 Chirality : 0.042 0.338 1523 Planarity : 0.004 0.058 1728 Dihedral : 7.736 99.214 1438 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.87 % Allowed : 11.73 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.23), residues: 1217 helix: -2.40 (0.17), residues: 791 sheet: -2.03 (0.70), residues: 57 loop : -1.92 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 601 HIS 0.004 0.001 HIS A 667 PHE 0.013 0.001 PHE A 673 TYR 0.014 0.001 TYR A 620 ARG 0.005 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 356) hydrogen bonds : angle 5.21411 ( 1020) covalent geometry : bond 0.00284 (10094) covalent geometry : angle 0.59228 (13645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 320 ILE cc_start: 0.8856 (pt) cc_final: 0.8457 (mt) REVERT: A 427 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 583 VAL cc_start: 0.8592 (t) cc_final: 0.8242 (m) REVERT: A 598 MET cc_start: 0.7338 (mtt) cc_final: 0.7036 (mtp) REVERT: A 611 GLN cc_start: 0.8218 (mm110) cc_final: 0.8010 (mm-40) REVERT: A 615 MET cc_start: 0.7539 (mmm) cc_final: 0.6922 (tpp) REVERT: A 622 ARG cc_start: 0.7938 (mmt180) cc_final: 0.7709 (mmt180) REVERT: B 406 TYR cc_start: 0.6832 (t80) cc_final: 0.6291 (t80) REVERT: B 615 MET cc_start: 0.8408 (mmm) cc_final: 0.8184 (mmt) outliers start: 9 outliers final: 5 residues processed: 141 average time/residue: 0.2493 time to fit residues: 48.6725 Evaluate side-chains 133 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 693 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 19 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS B 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.152963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112129 restraints weight = 13311.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108329 restraints weight = 12444.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109414 restraints weight = 15279.747| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10094 Z= 0.139 Angle : 0.586 10.251 13645 Z= 0.294 Chirality : 0.043 0.255 1523 Planarity : 0.003 0.052 1728 Dihedral : 7.136 79.799 1438 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.25 % Allowed : 14.33 % Favored : 84.42 % 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: -3.36 (0.23), residues: 1217 helix: -2.18 (0.17), residues: 791 sheet: -1.95 (0.71), residues: 57 loop : -1.89 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 326 HIS 0.005 0.001 HIS A 667 PHE 0.012 0.001 PHE A 673 TYR 0.013 0.001 TYR A 620 ARG 0.005 0.000 ARG A 163 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 356) hydrogen bonds : angle 4.90431 ( 1020) covalent geometry : bond 0.00329 (10094) covalent geometry : angle 0.58617 (13645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6646 (ttt90) cc_final: 0.6177 (mmt90) REVERT: A 320 ILE cc_start: 0.8760 (pt) cc_final: 0.8300 (mt) REVERT: A 427 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 598 MET cc_start: 0.7288 (mtt) cc_final: 0.7010 (mtp) REVERT: A 615 MET cc_start: 0.7604 (mmm) cc_final: 0.6925 (tpp) REVERT: A 622 ARG cc_start: 0.7918 (mmt180) cc_final: 0.7714 (mmt180) REVERT: B 615 MET cc_start: 0.8455 (mmm) cc_final: 0.8031 (mmt) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.2364 time to fit residues: 49.7189 Evaluate side-chains 136 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 693 THR Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114278 restraints weight = 13159.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110261 restraints weight = 11946.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111247 restraints weight = 14904.322| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10094 Z= 0.105 Angle : 0.558 10.458 13645 Z= 0.278 Chirality : 0.041 0.194 1523 Planarity : 0.003 0.050 1728 Dihedral : 6.524 58.553 1438 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.06 % Allowed : 16.35 % Favored : 82.60 % 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: -3.09 (0.23), residues: 1217 helix: -1.94 (0.17), residues: 792 sheet: -2.04 (0.73), residues: 55 loop : -1.81 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 595 HIS 0.005 0.001 HIS A 667 PHE 0.012 0.001 PHE A 673 TYR 0.011 0.001 TYR B 532 ARG 0.005 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.03121 ( 356) hydrogen bonds : angle 4.61715 ( 1020) covalent geometry : bond 0.00242 (10094) covalent geometry : angle 0.55844 (13645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6685 (ttt90) cc_final: 0.6173 (mmt90) REVERT: A 76 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7774 (tp) REVERT: A 320 ILE cc_start: 0.8741 (pt) cc_final: 0.8358 (mt) REVERT: A 427 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 581 ASP cc_start: 0.7425 (p0) cc_final: 0.7084 (p0) REVERT: A 583 VAL cc_start: 0.8489 (t) cc_final: 0.8048 (m) REVERT: A 598 MET cc_start: 0.7265 (mtt) cc_final: 0.6983 (mtp) REVERT: A 615 MET cc_start: 0.7547 (mmm) cc_final: 0.7007 (tpp) REVERT: A 622 ARG cc_start: 0.8034 (mmt180) cc_final: 0.7791 (mmt180) REVERT: A 660 ARG cc_start: 0.7140 (mmp80) cc_final: 0.6629 (mmt-90) REVERT: B 567 GLN cc_start: 0.8047 (mt0) cc_final: 0.7666 (mm-40) REVERT: B 615 MET cc_start: 0.8506 (mmm) cc_final: 0.8139 (mmt) outliers start: 11 outliers final: 5 residues processed: 147 average time/residue: 0.2556 time to fit residues: 51.2447 Evaluate side-chains 141 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114480 restraints weight = 13139.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110904 restraints weight = 11651.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112388 restraints weight = 11676.629| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10094 Z= 0.104 Angle : 0.557 10.187 13645 Z= 0.275 Chirality : 0.041 0.175 1523 Planarity : 0.003 0.049 1728 Dihedral : 6.299 53.137 1437 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.25 % Allowed : 17.50 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.24), residues: 1217 helix: -1.75 (0.17), residues: 798 sheet: -1.81 (0.73), residues: 57 loop : -1.66 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 595 HIS 0.005 0.001 HIS A 667 PHE 0.010 0.001 PHE A 673 TYR 0.016 0.001 TYR A 625 ARG 0.005 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 356) hydrogen bonds : angle 4.45978 ( 1020) covalent geometry : bond 0.00240 (10094) covalent geometry : angle 0.55677 (13645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6702 (ttt90) cc_final: 0.6183 (mmt90) REVERT: A 76 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 320 ILE cc_start: 0.8702 (pt) cc_final: 0.8372 (mt) REVERT: A 427 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7151 (mt-10) REVERT: A 581 ASP cc_start: 0.7471 (p0) cc_final: 0.5892 (t70) REVERT: A 583 VAL cc_start: 0.8402 (t) cc_final: 0.7965 (m) REVERT: A 598 MET cc_start: 0.7407 (mtt) cc_final: 0.7100 (mtp) REVERT: A 615 MET cc_start: 0.7504 (mmm) cc_final: 0.6982 (tpp) REVERT: A 660 ARG cc_start: 0.7128 (mmp80) cc_final: 0.6627 (mmt-90) REVERT: B 567 GLN cc_start: 0.8002 (mt0) cc_final: 0.7670 (mm-40) REVERT: B 615 MET cc_start: 0.8466 (mmm) cc_final: 0.8056 (mmt) outliers start: 13 outliers final: 11 residues processed: 155 average time/residue: 0.2769 time to fit residues: 59.7354 Evaluate side-chains 145 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 133 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.0370 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 121 optimal weight: 0.1980 chunk 28 optimal weight: 0.0770 chunk 116 optimal weight: 10.0000 overall best weight: 0.8218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114699 restraints weight = 13177.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.110952 restraints weight = 12600.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112256 restraints weight = 12662.040| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10094 Z= 0.101 Angle : 0.553 10.017 13645 Z= 0.274 Chirality : 0.041 0.171 1523 Planarity : 0.003 0.054 1728 Dihedral : 6.139 49.582 1437 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.25 % Allowed : 18.94 % Favored : 79.81 % 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: -2.70 (0.24), residues: 1217 helix: -1.61 (0.17), residues: 810 sheet: -1.75 (0.74), residues: 57 loop : -1.74 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 77 HIS 0.004 0.000 HIS A 667 PHE 0.011 0.001 PHE A 673 TYR 0.012 0.001 TYR A 625 ARG 0.007 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 356) hydrogen bonds : angle 4.36644 ( 1020) covalent geometry : bond 0.00233 (10094) covalent geometry : angle 0.55293 (13645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6756 (ttt90) cc_final: 0.6193 (mmt90) REVERT: A 76 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7600 (tp) REVERT: A 320 ILE cc_start: 0.8764 (pt) cc_final: 0.8474 (mt) REVERT: A 402 ILE cc_start: 0.8747 (pt) cc_final: 0.8389 (mt) REVERT: A 403 MET cc_start: 0.8350 (mmt) cc_final: 0.8083 (mmp) REVERT: A 427 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 581 ASP cc_start: 0.7625 (p0) cc_final: 0.6125 (t70) REVERT: A 583 VAL cc_start: 0.8360 (t) cc_final: 0.7872 (m) REVERT: A 598 MET cc_start: 0.7324 (mtt) cc_final: 0.7012 (mtp) REVERT: A 615 MET cc_start: 0.7480 (mmm) cc_final: 0.7001 (tpp) REVERT: A 660 ARG cc_start: 0.7103 (mmp80) cc_final: 0.6612 (mmt-90) REVERT: B 126 ASP cc_start: 0.7704 (p0) cc_final: 0.7244 (p0) REVERT: B 567 GLN cc_start: 0.8123 (mt0) cc_final: 0.7778 (mm-40) REVERT: B 615 MET cc_start: 0.8386 (mmm) cc_final: 0.8021 (mmt) outliers start: 13 outliers final: 11 residues processed: 152 average time/residue: 0.3165 time to fit residues: 67.2505 Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 49 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 43 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 118 optimal weight: 0.0000 overall best weight: 1.0366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.116907 restraints weight = 13135.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114657 restraints weight = 10555.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.116165 restraints weight = 10092.294| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10094 Z= 0.105 Angle : 0.546 9.862 13645 Z= 0.269 Chirality : 0.041 0.163 1523 Planarity : 0.003 0.054 1728 Dihedral : 6.116 48.776 1437 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.44 % Allowed : 19.23 % Favored : 79.33 % 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: -2.52 (0.24), residues: 1217 helix: -1.45 (0.18), residues: 809 sheet: -1.82 (0.74), residues: 57 loop : -1.71 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 77 HIS 0.005 0.001 HIS A 667 PHE 0.010 0.001 PHE A 673 TYR 0.009 0.001 TYR B 571 ARG 0.007 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.02871 ( 356) hydrogen bonds : angle 4.29661 ( 1020) covalent geometry : bond 0.00245 (10094) covalent geometry : angle 0.54599 (13645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6778 (ttt90) cc_final: 0.6228 (mmt90) REVERT: A 76 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7502 (tp) REVERT: A 320 ILE cc_start: 0.8707 (pt) cc_final: 0.8410 (mt) REVERT: A 402 ILE cc_start: 0.8680 (pt) cc_final: 0.8347 (mt) REVERT: A 403 MET cc_start: 0.8315 (mmt) cc_final: 0.8034 (mmp) REVERT: A 427 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7154 (mt-10) REVERT: A 581 ASP cc_start: 0.7585 (p0) cc_final: 0.6115 (t70) REVERT: A 583 VAL cc_start: 0.8355 (t) cc_final: 0.7881 (m) REVERT: A 598 MET cc_start: 0.7281 (mtt) cc_final: 0.6974 (mtp) REVERT: A 615 MET cc_start: 0.7411 (mmm) cc_final: 0.7054 (tpp) REVERT: A 660 ARG cc_start: 0.7087 (mmp80) cc_final: 0.6606 (mmt-90) REVERT: B 126 ASP cc_start: 0.7648 (p0) cc_final: 0.7209 (p0) REVERT: B 225 THR cc_start: 0.8510 (m) cc_final: 0.8055 (p) REVERT: B 567 GLN cc_start: 0.8150 (mt0) cc_final: 0.7829 (mm-40) REVERT: B 602 LYS cc_start: 0.7156 (mttt) cc_final: 0.6786 (mttp) outliers start: 15 outliers final: 11 residues processed: 148 average time/residue: 0.2420 time to fit residues: 49.6309 Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 79 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113781 restraints weight = 13181.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110275 restraints weight = 11639.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111424 restraints weight = 14007.441| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10094 Z= 0.128 Angle : 0.561 9.926 13645 Z= 0.277 Chirality : 0.042 0.163 1523 Planarity : 0.003 0.053 1728 Dihedral : 6.149 50.429 1437 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.25 % Allowed : 19.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.24), residues: 1217 helix: -1.41 (0.18), residues: 805 sheet: -1.95 (0.73), residues: 57 loop : -1.84 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 77 HIS 0.005 0.001 HIS A 667 PHE 0.010 0.001 PHE A 673 TYR 0.013 0.001 TYR B 296 ARG 0.006 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.03063 ( 356) hydrogen bonds : angle 4.29688 ( 1020) covalent geometry : bond 0.00307 (10094) covalent geometry : angle 0.56088 (13645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 1.261 Fit side-chains REVERT: A 69 ARG cc_start: 0.6708 (ttt90) cc_final: 0.6099 (mmt90) REVERT: A 76 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7492 (tp) REVERT: A 403 MET cc_start: 0.8297 (mmt) cc_final: 0.8075 (mmp) REVERT: A 427 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 581 ASP cc_start: 0.7625 (p0) cc_final: 0.6153 (t70) REVERT: A 583 VAL cc_start: 0.8373 (t) cc_final: 0.7893 (m) REVERT: A 598 MET cc_start: 0.7326 (mtt) cc_final: 0.7018 (mtp) REVERT: A 615 MET cc_start: 0.7482 (mmm) cc_final: 0.7110 (tpp) REVERT: A 660 ARG cc_start: 0.7088 (mmp80) cc_final: 0.6604 (mmt-90) REVERT: B 126 ASP cc_start: 0.7675 (p0) cc_final: 0.7256 (p0) REVERT: B 225 THR cc_start: 0.8434 (m) cc_final: 0.7954 (p) REVERT: B 567 GLN cc_start: 0.8110 (mt0) cc_final: 0.7801 (mm110) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.2801 time to fit residues: 57.4009 Evaluate side-chains 145 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 121 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117689 restraints weight = 13061.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114677 restraints weight = 10690.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116112 restraints weight = 11909.377| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10094 Z= 0.098 Angle : 0.545 9.779 13645 Z= 0.269 Chirality : 0.040 0.166 1523 Planarity : 0.003 0.056 1728 Dihedral : 5.973 45.221 1437 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.15 % Allowed : 19.42 % Favored : 79.42 % 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: -2.32 (0.24), residues: 1217 helix: -1.24 (0.18), residues: 810 sheet: -2.01 (0.72), residues: 57 loop : -1.73 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 77 HIS 0.005 0.000 HIS A 667 PHE 0.011 0.001 PHE A 673 TYR 0.012 0.001 TYR A 625 ARG 0.008 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.02781 ( 356) hydrogen bonds : angle 4.18540 ( 1020) covalent geometry : bond 0.00227 (10094) covalent geometry : angle 0.54506 (13645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 69 ARG cc_start: 0.6637 (ttt90) cc_final: 0.6076 (mmt90) REVERT: A 320 ILE cc_start: 0.8697 (pt) cc_final: 0.8367 (mt) REVERT: A 402 ILE cc_start: 0.8607 (pt) cc_final: 0.8320 (mt) REVERT: A 403 MET cc_start: 0.8267 (mmt) cc_final: 0.7957 (mmp) REVERT: A 427 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 581 ASP cc_start: 0.7643 (p0) cc_final: 0.6200 (t70) REVERT: A 583 VAL cc_start: 0.8361 (t) cc_final: 0.7881 (m) REVERT: A 598 MET cc_start: 0.7303 (mtt) cc_final: 0.7000 (mtp) REVERT: A 615 MET cc_start: 0.7307 (mmm) cc_final: 0.7092 (tpp) REVERT: A 660 ARG cc_start: 0.7076 (mmp80) cc_final: 0.6596 (mmt-90) REVERT: B 126 ASP cc_start: 0.7625 (p0) cc_final: 0.7193 (p0) REVERT: B 567 GLN cc_start: 0.7988 (mt0) cc_final: 0.7704 (mm110) REVERT: B 602 LYS cc_start: 0.7085 (mttt) cc_final: 0.6724 (mttp) REVERT: B 712 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7458 (tpt90) outliers start: 12 outliers final: 11 residues processed: 146 average time/residue: 0.2364 time to fit residues: 48.1260 Evaluate side-chains 146 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 700 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 89 optimal weight: 0.3980 chunk 73 optimal weight: 0.0050 chunk 6 optimal weight: 0.7980 chunk 108 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 502 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.157576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116076 restraints weight = 13085.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112372 restraints weight = 11451.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.113652 restraints weight = 13615.442| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10094 Z= 0.094 Angle : 0.545 9.750 13645 Z= 0.267 Chirality : 0.040 0.169 1523 Planarity : 0.003 0.058 1728 Dihedral : 5.836 44.811 1437 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.15 % Allowed : 19.62 % Favored : 79.23 % 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: -2.09 (0.24), residues: 1217 helix: -1.03 (0.18), residues: 806 sheet: -2.07 (0.71), residues: 57 loop : -1.72 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 77 HIS 0.006 0.000 HIS A 667 PHE 0.011 0.001 PHE A 673 TYR 0.011 0.001 TYR A 625 ARG 0.008 0.000 ARG B 622 Details of bonding type rmsd hydrogen bonds : bond 0.02688 ( 356) hydrogen bonds : angle 4.14684 ( 1020) covalent geometry : bond 0.00213 (10094) covalent geometry : angle 0.54526 (13645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.08 seconds wall clock time: 66 minutes 41.26 seconds (4001.26 seconds total)