Starting phenix.real_space_refine on Sat Jul 4 18:48:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.map" model { file = "/net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4i_62060/07_2026/9k4i_62060.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 Ca 3 9.91 5 S 124 5.16 5 C 14479 2.51 5 N 3623 2.21 5 O 3963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22192 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5563 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5239 Classifications: {'peptide': 651} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 634} Chain breaks: 5 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5563 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 5563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 686, 5563 Classifications: {'peptide': 686} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 661} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'YZY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.23 Number of scatterers: 22192 At special positions: 0 Unit cell: (120.35, 142.76, 137.78, 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) Ca 3 19.99 S 124 16.00 O 3963 8.00 N 3623 7.00 C 14479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 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: 2.03 Conformation dependent library (CDL) restraints added in 954.8 milliseconds 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5212 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 3 sheets defined 79.5% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.508A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.625A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 removed outlier: 4.706A pdb=" N GLU A 186 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 340 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 354 through 362 removed outlier: 3.572A pdb=" N ILE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 385 removed outlier: 3.779A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 433 Proline residue: A 409 - end of helix removed outlier: 6.547A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N THR A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 458 removed outlier: 3.790A pdb=" N MET A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 450 " --> pdb=" O TYR A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.157A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 492 through 497' Processing helix chain 'A' and resid 498 through 500 No H-bonds generated for 'chain 'A' and resid 498 through 500' Processing helix chain 'A' and resid 502 through 540 removed outlier: 3.733A pdb=" N LEU A 506 " --> pdb=" O HIS A 502 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 584 through 589 removed outlier: 3.787A pdb=" N ASN A 589 " --> pdb=" O TYR A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 652 removed outlier: 3.822A pdb=" N ASP A 633 " --> pdb=" O GLN A 629 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASP A 636 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 663 removed outlier: 4.192A pdb=" N ASN A 662 " --> pdb=" O PRO A 659 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 663 " --> pdb=" O PRO A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 735 Processing helix chain 'A' and resid 739 through 761 Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 59 through 71 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.585A pdb=" N ASN B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 104 removed outlier: 4.352A pdb=" N LEU B 102 " --> pdb=" O ASP B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 171 through 181 removed outlier: 4.282A pdb=" N GLN B 181 " --> pdb=" O MET B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 Processing helix chain 'B' and resid 205 through 221 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 254 through 275 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.541A pdb=" N LEU B 282 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 318 through 324 Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.975A pdb=" N ARG B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 Processing helix chain 'B' and resid 360 through 371 Processing helix chain 'B' and resid 374 through 380 removed outlier: 3.611A pdb=" N ILE B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 407 removed outlier: 4.078A pdb=" N SER B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 446 Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.758A pdb=" N GLU B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 480 removed outlier: 3.578A pdb=" N VAL B 461 " --> pdb=" O GLN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 493 through 513 removed outlier: 3.813A pdb=" N LEU B 513 " --> pdb=" O SER B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 520 Processing helix chain 'B' and resid 522 through 560 removed outlier: 4.551A pdb=" N LEU B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP B 536 " --> pdb=" O GLN B 532 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.824A pdb=" N HIS B 585 " --> pdb=" O ASN B 581 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 586 " --> pdb=" O ASP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 586' Processing helix chain 'B' and resid 587 through 599 removed outlier: 4.366A pdb=" N PHE B 599 " --> pdb=" O PHE B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 635 Processing helix chain 'B' and resid 635 through 673 removed outlier: 3.525A pdb=" N LEU B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS B 655 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS B 658 " --> pdb=" O ASN B 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 670 " --> pdb=" O LYS B 666 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.519A pdb=" N ILE B 684 " --> pdb=" O PRO B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 754 Processing helix chain 'B' and resid 757 through 779 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 109 through 117 removed outlier: 3.796A pdb=" N GLU C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.752A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 340 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.509A pdb=" N ILE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.602A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 433 Proline residue: C 409 - end of helix removed outlier: 5.849A pdb=" N PHE C 427 " --> pdb=" O TRP C 423 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N THR C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 459 removed outlier: 3.850A pdb=" N LEU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 438 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 502 through 540 removed outlier: 4.201A pdb=" N LEU C 506 " --> pdb=" O HIS C 502 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 567 through 579 Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.657A pdb=" N VAL C 587 " --> pdb=" O ASN C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 613 Processing helix chain 'C' and resid 615 through 634 removed outlier: 3.575A pdb=" N ASP C 633 " --> pdb=" O GLN C 629 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS C 634 " --> pdb=" O LEU C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 652 Processing helix chain 'C' and resid 703 through 735 Processing helix chain 'C' and resid 739 through 762 removed outlier: 3.559A pdb=" N PHE C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 removed outlier: 3.634A pdb=" N ILE D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.552A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 340 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 354 through 362 removed outlier: 3.620A pdb=" N ILE D 360 " --> pdb=" O LEU D 356 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS D 361 " --> pdb=" O GLY D 357 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 385 removed outlier: 3.734A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 433 Processing helix chain 'D' and resid 433 through 458 removed outlier: 3.657A pdb=" N LEU D 437 " --> pdb=" O ASP D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 502 through 540 removed outlier: 4.176A pdb=" N LEU D 506 " --> pdb=" O HIS D 502 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 567 through 580 removed outlier: 3.962A pdb=" N PHE D 580 " --> pdb=" O PHE D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.700A pdb=" N VAL D 587 " --> pdb=" O ASN D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 613 Processing helix chain 'D' and resid 615 through 634 removed outlier: 3.636A pdb=" N ASP D 633 " --> pdb=" O GLN D 629 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS D 634 " --> pdb=" O LEU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 651 removed outlier: 3.551A pdb=" N ALA D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 662 removed outlier: 3.749A pdb=" N PHE D 661 " --> pdb=" O PRO D 658 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN D 662 " --> pdb=" O PRO D 659 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 658 through 662' Processing helix chain 'D' and resid 703 through 735 Processing helix chain 'D' and resid 739 through 762 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 4.258A pdb=" N VAL B 183 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.525A pdb=" N VAL A 166 " --> pdb=" O LEU D 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 20 removed outlier: 4.832A pdb=" N VAL D 166 " --> pdb=" O LEU C 20 " (cutoff:3.500A) 1502 hydrogen bonds defined for protein. 4374 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: 4.14 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3578 1.29 - 1.42: 5936 1.42 - 1.55: 12985 1.55 - 1.69: 0 1.69 - 1.82: 198 Bond restraints: 22697 Sorted by residual: bond pdb=" C12 YZY B1101 " pdb=" C13 YZY B1101 " ideal model delta sigma weight residual 1.524 1.308 0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C12 YZY C 804 " pdb=" C13 YZY C 804 " ideal model delta sigma weight residual 1.524 1.309 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C12 YZY A 803 " pdb=" C13 YZY A 803 " ideal model delta sigma weight residual 1.524 1.310 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C12 YZY C 803 " pdb=" C13 YZY C 803 " ideal model delta sigma weight residual 1.524 1.310 0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C29 YZY C 804 " pdb=" C30 YZY C 804 " ideal model delta sigma weight residual 1.497 1.324 0.173 2.00e-02 2.50e+03 7.47e+01 ... (remaining 22692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 30423 3.86 - 7.72: 264 7.72 - 11.59: 30 11.59 - 15.45: 13 15.45 - 19.31: 4 Bond angle restraints: 30734 Sorted by residual: angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 115.73 103.06 12.67 1.59e+00 3.96e-01 6.35e+01 angle pdb=" N ALA D 111 " pdb=" CA ALA D 111 " pdb=" C ALA D 111 " ideal model delta sigma weight residual 113.19 104.81 8.38 1.19e+00 7.06e-01 4.96e+01 angle pdb=" C27 YZY B1101 " pdb=" C28 YZY B1101 " pdb=" C29 YZY B1101 " ideal model delta sigma weight residual 128.13 108.82 19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C27 YZY A 803 " pdb=" C28 YZY A 803 " pdb=" C29 YZY A 803 " ideal model delta sigma weight residual 128.13 108.83 19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" C27 YZY C 803 " pdb=" C28 YZY C 803 " pdb=" C29 YZY C 803 " ideal model delta sigma weight residual 128.13 108.89 19.24 3.00e+00 1.11e-01 4.11e+01 ... (remaining 30729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.83: 13569 32.83 - 65.67: 117 65.67 - 98.50: 25 98.50 - 131.34: 4 131.34 - 164.17: 8 Dihedral angle restraints: 13723 sinusoidal: 5711 harmonic: 8012 Sorted by residual: dihedral pdb=" C5 YZY B1101 " pdb=" C3 YZY B1101 " pdb=" C4 YZY B1101 " pdb=" O2 YZY B1101 " ideal model delta sinusoidal sigma weight residual 177.74 13.57 164.17 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY C 803 " pdb=" C3 YZY C 803 " pdb=" C4 YZY C 803 " pdb=" O2 YZY C 803 " ideal model delta sinusoidal sigma weight residual 177.74 13.57 164.17 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C5 YZY A 803 " pdb=" C3 YZY A 803 " pdb=" C4 YZY A 803 " pdb=" O2 YZY A 803 " ideal model delta sinusoidal sigma weight residual 177.74 13.66 164.08 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2689 0.046 - 0.092: 602 0.092 - 0.139: 158 0.139 - 0.185: 20 0.185 - 0.231: 9 Chirality restraints: 3478 Sorted by residual: chirality pdb=" CBI Y01 C 802 " pdb=" CAU Y01 C 802 " pdb=" CBE Y01 C 802 " pdb=" CBG Y01 C 802 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CBI Y01 A 802 " pdb=" CAU Y01 A 802 " pdb=" CBE Y01 A 802 " pdb=" CBG Y01 A 802 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CBI Y01 D 802 " pdb=" CAU Y01 D 802 " pdb=" CBE Y01 D 802 " pdb=" CBG Y01 D 802 " both_signs ideal model delta sigma weight residual False 2.94 2.71 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3475 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 568 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C LEU A 568 " 0.065 2.00e-02 2.50e+03 pdb=" O LEU A 568 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE A 569 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 83 " -0.014 2.00e-02 2.50e+03 2.83e-02 7.98e+00 pdb=" C LEU C 83 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU C 83 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU C 84 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 384 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ALA C 384 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA C 384 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 385 " -0.016 2.00e-02 2.50e+03 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 193 2.58 - 3.16: 23198 3.16 - 3.74: 35693 3.74 - 4.32: 52433 4.32 - 4.90: 82207 Nonbonded interactions: 193724 Sorted by model distance: nonbonded pdb=" OE1 GLU D 421 " pdb="CA CA D 801 " model vdw 1.996 3.250 nonbonded pdb=" O THR A 734 " pdb=" OD1 ASN A 735 " model vdw 2.169 3.040 nonbonded pdb=" OD1 ASP C 188 " pdb=" OG SER D 262 " model vdw 2.263 3.040 nonbonded pdb=" OAH Y01 D 802 " pdb=" OAW Y01 D 802 " model vdw 2.268 3.040 nonbonded pdb=" OAH Y01 C 802 " pdb=" OAW Y01 C 802 " model vdw 2.269 3.040 ... (remaining 193719 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 16 through 802) selection = (chain 'C' and resid 16 through 802) selection = chain 'D' } 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: 4.530 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.000 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.010 0.216 22700 Z= 0.700 Angle : 1.105 19.310 30740 Z= 0.731 Chirality : 0.043 0.231 3478 Planarity : 0.004 0.045 3820 Dihedral : 11.956 164.173 8502 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.25 % Allowed : 2.67 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2673 helix: 0.01 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : -1.87 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 17 TYR 0.016 0.001 TYR A 541 PHE 0.014 0.001 PHE B 321 TRP 0.010 0.001 TRP C 225 HIS 0.004 0.001 HIS C 387 Details of bonding type rmsd/Z covalent geometry : bond 0.01002 / 0.70 (22697) covalent geometry : angle 1.10465 / 0.73 (30734) SS BOND : bond 0.00246 / 0.12 ( 3) SS BOND : angle 0.45900 / 0.26 ( 6) hydrogen bonds : bond 0.18440 / 12.23 ( 1502) hydrogen bonds : angle 7.11995 / 5.18 ( 4374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 615 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 TYR cc_start: 0.7993 (m-80) cc_final: 0.7750 (m-80) REVERT: A 423 TRP cc_start: 0.8208 (t-100) cc_final: 0.7528 (t60) REVERT: A 465 PRO cc_start: 0.8554 (Cg_exo) cc_final: 0.8350 (Cg_endo) REVERT: B 63 VAL cc_start: 0.7514 (t) cc_final: 0.7283 (t) REVERT: B 443 TRP cc_start: 0.8145 (t60) cc_final: 0.7872 (t60) REVERT: B 481 HIS cc_start: 0.6014 (p-80) cc_final: 0.5602 (p-80) REVERT: B 606 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8009 (mt) REVERT: B 675 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8486 (mmpt) REVERT: B 724 LYS cc_start: 0.8667 (ttpt) cc_final: 0.8364 (tmtt) REVERT: D 744 LYS cc_start: 0.8903 (mmtm) cc_final: 0.8508 (mmtp) outliers start: 6 outliers final: 4 residues processed: 619 average time/residue: 0.6514 time to fit residues: 460.2256 Evaluate side-chains 335 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 330 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 759 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 GLN A 386 GLN ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN B 390 HIS B 557 GLN B 618 GLN B 654 ASN B 732 GLN B 766 GLN C 62 ASN C 432 HIS C 629 GLN C 748 GLN ** D 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 GLN ** D 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.083565 restraints weight = 38824.195| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.72 r_work: 0.2962 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22700 Z= 0.146 Angle : 0.574 11.043 30740 Z= 0.300 Chirality : 0.039 0.363 3478 Planarity : 0.004 0.047 3820 Dihedral : 11.707 179.594 3272 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.17 % Allowed : 12.94 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.16), residues: 2673 helix: 2.19 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.18 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 211 TYR 0.016 0.001 TYR B 368 PHE 0.022 0.002 PHE A 427 TRP 0.019 0.001 TRP C 327 HIS 0.021 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (22697) covalent geometry : angle 0.57358 / 0.30 (30734) SS BOND : bond 0.00313 / 0.15 ( 3) SS BOND : angle 0.55750 / 0.32 ( 6) hydrogen bonds : bond 0.05159 / 3.43 ( 1502) hydrogen bonds : angle 4.39041 / 3.21 ( 4374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 410 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8562 (t70) cc_final: 0.8336 (t0) REVERT: A 81 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8166 (mt-10) REVERT: A 102 TYR cc_start: 0.8493 (m-80) cc_final: 0.8047 (m-80) REVERT: A 238 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8380 (ttmp) REVERT: A 327 TRP cc_start: 0.8863 (p-90) cc_final: 0.8452 (p-90) REVERT: A 339 PHE cc_start: 0.9085 (m-80) cc_final: 0.8798 (m-80) REVERT: A 394 HIS cc_start: 0.7531 (m-70) cc_final: 0.7255 (m-70) REVERT: A 400 PRO cc_start: 0.8516 (Cg_exo) cc_final: 0.8180 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8367 (t-100) cc_final: 0.7588 (t60) REVERT: A 512 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7406 (mmp-170) REVERT: A 629 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: A 709 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8043 (pt0) REVERT: A 738 LEU cc_start: 0.8880 (mt) cc_final: 0.8642 (mp) REVERT: B 53 LEU cc_start: 0.8264 (tp) cc_final: 0.8035 (tm) REVERT: B 112 ASP cc_start: 0.8425 (p0) cc_final: 0.8049 (p0) REVERT: B 481 HIS cc_start: 0.6304 (p-80) cc_final: 0.6093 (t70) REVERT: B 504 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6843 (t80) REVERT: B 530 MET cc_start: 0.7645 (mtt) cc_final: 0.6426 (tmt) REVERT: B 606 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 724 LYS cc_start: 0.8466 (ttpt) cc_final: 0.7836 (tptt) REVERT: B 727 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7734 (ptp-170) REVERT: B 759 GLU cc_start: 0.8429 (tp30) cc_final: 0.8225 (tp30) REVERT: C 17 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7701 (mmm160) REVERT: C 32 GLU cc_start: 0.8853 (mp0) cc_final: 0.8545 (pm20) REVERT: C 66 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8947 (mmm) REVERT: C 118 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: C 229 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: C 247 GLN cc_start: 0.9122 (tt0) cc_final: 0.8870 (tt0) REVERT: C 286 ASP cc_start: 0.8423 (t0) cc_final: 0.7729 (t0) REVERT: C 331 LEU cc_start: 0.8926 (tp) cc_final: 0.8693 (tp) REVERT: C 339 PHE cc_start: 0.9079 (m-80) cc_final: 0.8877 (t80) REVERT: C 430 TYR cc_start: 0.8171 (t80) cc_final: 0.7871 (t80) REVERT: C 432 HIS cc_start: 0.8504 (m90) cc_final: 0.8272 (m-70) REVERT: C 450 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 491 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 595 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: C 636 ASP cc_start: 0.9018 (m-30) cc_final: 0.8699 (p0) REVERT: C 711 GLN cc_start: 0.8626 (tp40) cc_final: 0.8363 (tp40) REVERT: D 50 GLN cc_start: 0.8953 (tt0) cc_final: 0.8462 (tp40) REVERT: D 66 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8420 (mtp) REVERT: D 177 ASN cc_start: 0.9182 (p0) cc_final: 0.8968 (p0) REVERT: D 343 MET cc_start: 0.8450 (tpt) cc_final: 0.8099 (tpt) REVERT: D 358 LEU cc_start: 0.8956 (mt) cc_final: 0.8658 (mm) REVERT: D 394 HIS cc_start: 0.7922 (m-70) cc_final: 0.7656 (m-70) REVERT: D 657 LEU cc_start: 0.8389 (mp) cc_final: 0.8167 (mp) REVERT: D 744 LYS cc_start: 0.9040 (mmtm) cc_final: 0.8739 (mmtm) outliers start: 76 outliers final: 13 residues processed: 454 average time/residue: 0.6173 time to fit residues: 322.2672 Evaluate side-chains 341 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 315 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 759 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 208 optimal weight: 4.9990 chunk 213 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 205 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 165 optimal weight: 0.3980 chunk 203 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 308 GLN A 432 HIS A 748 GLN B 766 GLN C 629 GLN C 748 GLN D 192 HIS D 306 ASN D 625 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.113505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081939 restraints weight = 39450.166| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.70 r_work: 0.2916 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22700 Z= 0.146 Angle : 0.538 8.385 30740 Z= 0.281 Chirality : 0.038 0.318 3478 Planarity : 0.004 0.067 3820 Dihedral : 10.117 178.302 3266 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.01 % Allowed : 14.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.16), residues: 2673 helix: 2.47 (0.11), residues: 1961 sheet: None (None), residues: 0 loop : 0.26 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 324 TYR 0.015 0.001 TYR C 460 PHE 0.018 0.001 PHE B 544 TRP 0.028 0.001 TRP A 327 HIS 0.016 0.001 HIS A 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (22697) covalent geometry : angle 0.53808 / 0.28 (30734) SS BOND : bond 0.00190 / 0.10 ( 3) SS BOND : angle 0.53750 / 0.39 ( 6) hydrogen bonds : bond 0.04772 / 3.16 ( 1502) hydrogen bonds : angle 4.07923 / 3.00 ( 4374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 359 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 102 TYR cc_start: 0.8686 (m-80) cc_final: 0.8192 (m-80) REVERT: A 327 TRP cc_start: 0.8683 (p-90) cc_final: 0.8378 (p-90) REVERT: A 390 ARG cc_start: 0.7617 (ptt-90) cc_final: 0.7370 (tmt-80) REVERT: A 400 PRO cc_start: 0.8515 (Cg_exo) cc_final: 0.8167 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8303 (t-100) cc_final: 0.7455 (t60) REVERT: A 432 HIS cc_start: 0.8615 (m90) cc_final: 0.8395 (m-70) REVERT: A 629 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7586 (mp-120) REVERT: A 709 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8027 (pt0) REVERT: A 733 LYS cc_start: 0.8668 (mttm) cc_final: 0.8416 (mtmt) REVERT: A 748 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8639 (tm-30) REVERT: B 53 LEU cc_start: 0.8358 (tp) cc_final: 0.8114 (tm) REVERT: B 112 ASP cc_start: 0.8384 (p0) cc_final: 0.8006 (p0) REVERT: B 260 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: B 425 TYR cc_start: 0.7876 (m-80) cc_final: 0.7602 (m-80) REVERT: B 504 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6912 (t80) REVERT: B 530 MET cc_start: 0.7897 (mtt) cc_final: 0.6731 (pp-130) REVERT: B 606 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8393 (mt) REVERT: B 724 LYS cc_start: 0.8451 (ttpt) cc_final: 0.7844 (tptt) REVERT: B 727 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7945 (ptp-170) REVERT: C 17 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7811 (mmm160) REVERT: C 118 TYR cc_start: 0.7580 (OUTLIER) cc_final: 0.7021 (m-80) REVERT: C 173 GLN cc_start: 0.7857 (pp30) cc_final: 0.7654 (pm20) REVERT: C 229 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: C 247 GLN cc_start: 0.9187 (tt0) cc_final: 0.8986 (tt0) REVERT: C 286 ASP cc_start: 0.8562 (t0) cc_final: 0.7788 (t0) REVERT: C 335 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8739 (mpp) REVERT: C 421 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7694 (pt0) REVERT: C 450 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7985 (mm) REVERT: C 513 MET cc_start: 0.7985 (mtm) cc_final: 0.7475 (mtm) REVERT: C 711 GLN cc_start: 0.8656 (tp40) cc_final: 0.8301 (tp40) REVERT: D 50 GLN cc_start: 0.8988 (tt0) cc_final: 0.8526 (tp-100) REVERT: D 324 ARG cc_start: 0.7956 (ptm160) cc_final: 0.7545 (ptm160) REVERT: D 339 PHE cc_start: 0.9204 (m-80) cc_final: 0.8992 (m-80) REVERT: D 343 MET cc_start: 0.8413 (tpt) cc_final: 0.8098 (tpt) REVERT: D 359 PHE cc_start: 0.8555 (t80) cc_final: 0.8158 (t80) REVERT: D 548 ASP cc_start: 0.8981 (t0) cc_final: 0.8776 (t0) REVERT: D 551 ASN cc_start: 0.9012 (t0) cc_final: 0.8702 (t0) REVERT: D 736 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8670 (mt-10) REVERT: D 740 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 744 LYS cc_start: 0.9197 (mmtm) cc_final: 0.8990 (mmtm) outliers start: 96 outliers final: 25 residues processed: 425 average time/residue: 0.5710 time to fit residues: 281.4941 Evaluate side-chains 348 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 312 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 748 GLN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 172 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 chunk 132 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 654 ASN B 766 GLN C 92 HIS C 432 HIS C 629 GLN C 742 ASN C 748 GLN D 82 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.081574 restraints weight = 39367.102| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.76 r_work: 0.2923 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22700 Z= 0.124 Angle : 0.526 9.168 30740 Z= 0.270 Chirality : 0.037 0.338 3478 Planarity : 0.004 0.060 3820 Dihedral : 8.978 174.044 3266 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.42 % Allowed : 16.53 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.16), residues: 2673 helix: 2.53 (0.11), residues: 1961 sheet: None (None), residues: 0 loop : 0.42 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 255 TYR 0.015 0.001 TYR D 430 PHE 0.023 0.001 PHE A 427 TRP 0.018 0.001 TRP A 327 HIS 0.022 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (22697) covalent geometry : angle 0.52553 / 0.27 (30734) SS BOND : bond 0.00171 / 0.08 ( 3) SS BOND : angle 0.35896 / 0.24 ( 6) hydrogen bonds : bond 0.04304 / 2.85 ( 1502) hydrogen bonds : angle 3.93744 / 2.91 ( 4374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 340 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8357 (mt-10) REVERT: A 102 TYR cc_start: 0.8700 (m-80) cc_final: 0.8177 (m-80) REVERT: A 327 TRP cc_start: 0.8733 (p-90) cc_final: 0.8509 (p-90) REVERT: A 394 HIS cc_start: 0.7808 (m-70) cc_final: 0.7564 (m-70) REVERT: A 400 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8106 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8276 (t-100) cc_final: 0.7463 (t60) REVERT: A 468 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8752 (tt0) REVERT: A 512 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7384 (mmp-170) REVERT: A 629 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: A 709 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8041 (pt0) REVERT: B 53 LEU cc_start: 0.8353 (tp) cc_final: 0.8106 (tm) REVERT: B 112 ASP cc_start: 0.8357 (p0) cc_final: 0.7990 (p0) REVERT: B 260 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: B 425 TYR cc_start: 0.7939 (m-80) cc_final: 0.7575 (m-80) REVERT: B 504 PHE cc_start: 0.7508 (OUTLIER) cc_final: 0.7034 (t80) REVERT: B 530 MET cc_start: 0.7813 (mtt) cc_final: 0.6702 (tmm) REVERT: B 606 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 724 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7867 (tptt) REVERT: B 727 ARG cc_start: 0.8404 (mtp85) cc_final: 0.7920 (ptp-170) REVERT: B 729 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8811 (mm-30) REVERT: C 17 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7814 (mmm160) REVERT: C 118 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: C 286 ASP cc_start: 0.8531 (t0) cc_final: 0.7691 (t0) REVERT: C 335 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8719 (mpp) REVERT: C 421 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: C 430 TYR cc_start: 0.8389 (t80) cc_final: 0.8058 (t80) REVERT: C 432 HIS cc_start: 0.8619 (m90) cc_final: 0.8387 (m-70) REVERT: C 711 GLN cc_start: 0.8664 (tp40) cc_final: 0.8285 (tp40) REVERT: D 50 GLN cc_start: 0.8976 (tt0) cc_final: 0.8518 (tp-100) REVERT: D 66 MET cc_start: 0.8939 (mmm) cc_final: 0.8293 (mmm) REVERT: D 331 LEU cc_start: 0.9301 (tt) cc_final: 0.9094 (tp) REVERT: D 343 MET cc_start: 0.8462 (tpt) cc_final: 0.8096 (tpt) REVERT: D 359 PHE cc_start: 0.8520 (t80) cc_final: 0.8140 (t80) REVERT: D 380 MET cc_start: 0.8548 (mmm) cc_final: 0.8311 (mtm) REVERT: D 512 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8284 (tpm170) REVERT: D 541 TYR cc_start: 0.8806 (m-80) cc_final: 0.8295 (m-10) REVERT: D 551 ASN cc_start: 0.9041 (t0) cc_final: 0.8679 (t0) REVERT: D 736 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8671 (mt-10) REVERT: D 740 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 744 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8856 (mmtm) outliers start: 82 outliers final: 32 residues processed: 389 average time/residue: 0.5702 time to fit residues: 255.7067 Evaluate side-chains 355 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 311 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 512 ARG Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 736 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 5 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 256 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS A 436 ASN B 96 ASN B 766 GLN C 629 GLN C 735 ASN ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.081461 restraints weight = 39190.703| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.77 r_work: 0.2925 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22700 Z= 0.123 Angle : 0.519 9.449 30740 Z= 0.267 Chirality : 0.037 0.304 3478 Planarity : 0.004 0.053 3820 Dihedral : 8.371 170.634 3266 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.01 % Allowed : 16.87 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.16), residues: 2673 helix: 2.56 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : 0.38 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 441 TYR 0.016 0.001 TYR C 524 PHE 0.018 0.001 PHE C 319 TRP 0.021 0.001 TRP C 322 HIS 0.021 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (22697) covalent geometry : angle 0.51937 / 0.27 (30734) SS BOND : bond 0.00320 / 0.15 ( 3) SS BOND : angle 0.41326 / 0.21 ( 6) hydrogen bonds : bond 0.04157 / 2.75 ( 1502) hydrogen bonds : angle 3.85649 / 2.85 ( 4374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 338 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 102 TYR cc_start: 0.8762 (m-80) cc_final: 0.7680 (m-80) REVERT: A 327 TRP cc_start: 0.8715 (p-90) cc_final: 0.8477 (p-90) REVERT: A 394 HIS cc_start: 0.7813 (m-70) cc_final: 0.7558 (m-70) REVERT: A 400 PRO cc_start: 0.8469 (Cg_exo) cc_final: 0.8111 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 423 TRP cc_start: 0.8231 (t-100) cc_final: 0.7402 (t60) REVERT: A 432 HIS cc_start: 0.8620 (m90) cc_final: 0.8417 (m-70) REVERT: A 468 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8730 (tt0) REVERT: A 709 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8072 (pt0) REVERT: B 53 LEU cc_start: 0.8281 (tp) cc_final: 0.8043 (tm) REVERT: B 112 ASP cc_start: 0.8325 (p0) cc_final: 0.7961 (p0) REVERT: B 260 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: B 425 TYR cc_start: 0.7977 (m-80) cc_final: 0.7584 (m-80) REVERT: B 504 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7044 (t80) REVERT: B 530 MET cc_start: 0.7714 (mtt) cc_final: 0.6691 (ttp) REVERT: B 535 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8613 (pp30) REVERT: B 588 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7115 (tt) REVERT: B 606 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8333 (mt) REVERT: B 724 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7781 (tptm) REVERT: B 727 ARG cc_start: 0.8412 (mtp85) cc_final: 0.7733 (ptp-170) REVERT: B 729 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8846 (mm-30) REVERT: B 759 GLU cc_start: 0.8732 (tp30) cc_final: 0.8450 (tp30) REVERT: C 17 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7763 (mmm160) REVERT: C 118 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: C 180 GLU cc_start: 0.8399 (pp20) cc_final: 0.8157 (pp20) REVERT: C 229 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: C 286 ASP cc_start: 0.8586 (t0) cc_final: 0.7794 (t0) REVERT: C 335 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8708 (mpp) REVERT: C 421 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7601 (pt0) REVERT: C 430 TYR cc_start: 0.8253 (t80) cc_final: 0.7078 (t80) REVERT: C 529 LEU cc_start: 0.8760 (tp) cc_final: 0.8531 (mt) REVERT: C 705 ASP cc_start: 0.7896 (t0) cc_final: 0.7628 (t0) REVERT: C 711 GLN cc_start: 0.8662 (tp40) cc_final: 0.8336 (tp40) REVERT: D 50 GLN cc_start: 0.8995 (tt0) cc_final: 0.8541 (tp-100) REVERT: D 66 MET cc_start: 0.9024 (mmm) cc_final: 0.8476 (mmm) REVERT: D 81 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8608 (mt-10) REVERT: D 177 ASN cc_start: 0.9173 (p0) cc_final: 0.8934 (p0) REVERT: D 324 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7683 (ptm160) REVERT: D 343 MET cc_start: 0.8474 (tpt) cc_final: 0.8138 (tpt) REVERT: D 358 LEU cc_start: 0.8941 (mt) cc_final: 0.8640 (mm) REVERT: D 359 PHE cc_start: 0.8479 (t80) cc_final: 0.8032 (t80) REVERT: D 380 MET cc_start: 0.8541 (mmm) cc_final: 0.8241 (mtm) REVERT: D 541 TYR cc_start: 0.8796 (m-80) cc_final: 0.8309 (m-10) REVERT: D 736 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: D 740 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 744 LYS cc_start: 0.9188 (mmtm) cc_final: 0.8838 (mmtm) outliers start: 96 outliers final: 34 residues processed: 401 average time/residue: 0.5990 time to fit residues: 277.0261 Evaluate side-chains 351 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 304 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 17 optimal weight: 1.9990 chunk 219 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 196 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 654 ASN B 766 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C 748 GLN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.111169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.078790 restraints weight = 39476.338| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.72 r_work: 0.2877 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22700 Z= 0.172 Angle : 0.566 12.815 30740 Z= 0.287 Chirality : 0.039 0.289 3478 Planarity : 0.004 0.048 3820 Dihedral : 8.225 169.820 3266 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.26 % Allowed : 17.62 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.16), residues: 2673 helix: 2.46 (0.11), residues: 1965 sheet: None (None), residues: 0 loop : 0.30 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 324 TYR 0.020 0.001 TYR C 524 PHE 0.019 0.001 PHE D 341 TRP 0.022 0.001 TRP C 322 HIS 0.022 0.001 HIS D 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (22697) covalent geometry : angle 0.56586 / 0.29 (30734) SS BOND : bond 0.00221 / 0.11 ( 3) SS BOND : angle 0.96797 / 0.50 ( 6) hydrogen bonds : bond 0.04562 / 3.01 ( 1502) hydrogen bonds : angle 3.92309 / 2.89 ( 4374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 319 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8319 (mt-10) REVERT: A 102 TYR cc_start: 0.8968 (m-80) cc_final: 0.8758 (m-80) REVERT: A 394 HIS cc_start: 0.7836 (m-70) cc_final: 0.7583 (m-70) REVERT: A 400 PRO cc_start: 0.8521 (Cg_exo) cc_final: 0.8196 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 423 TRP cc_start: 0.8204 (t-100) cc_final: 0.7372 (t60) REVERT: A 432 HIS cc_start: 0.8763 (m90) cc_final: 0.8534 (m-70) REVERT: A 492 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8052 (mtp180) REVERT: A 512 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7431 (mmp-170) REVERT: A 709 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8159 (tt0) REVERT: B 53 LEU cc_start: 0.8324 (tp) cc_final: 0.8068 (tm) REVERT: B 112 ASP cc_start: 0.8340 (p0) cc_final: 0.8013 (p0) REVERT: B 260 GLU cc_start: 0.8623 (mp0) cc_final: 0.8337 (mp0) REVERT: B 425 TYR cc_start: 0.8037 (m-80) cc_final: 0.7686 (m-80) REVERT: B 504 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7106 (t80) REVERT: B 530 MET cc_start: 0.7857 (mtt) cc_final: 0.6792 (ttp) REVERT: B 535 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8653 (pp30) REVERT: B 588 ILE cc_start: 0.7504 (OUTLIER) cc_final: 0.7141 (tt) REVERT: B 606 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8391 (mt) REVERT: B 724 LYS cc_start: 0.8444 (ttpt) cc_final: 0.7981 (tptm) REVERT: B 727 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8119 (mtm-85) REVERT: B 729 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8839 (mm-30) REVERT: B 759 GLU cc_start: 0.8778 (tp30) cc_final: 0.8508 (tp30) REVERT: C 17 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7768 (mmm160) REVERT: C 118 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7196 (m-80) REVERT: C 180 GLU cc_start: 0.8392 (pp20) cc_final: 0.8136 (pp20) REVERT: C 229 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: C 286 ASP cc_start: 0.8617 (t0) cc_final: 0.7874 (t0) REVERT: C 335 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8706 (mpp) REVERT: C 416 TRP cc_start: 0.8572 (t-100) cc_final: 0.8234 (t-100) REVERT: C 421 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: C 430 TYR cc_start: 0.8239 (t80) cc_final: 0.7820 (t80) REVERT: C 432 HIS cc_start: 0.8739 (m-70) cc_final: 0.8455 (m-70) REVERT: C 705 ASP cc_start: 0.7952 (t0) cc_final: 0.7673 (t0) REVERT: C 711 GLN cc_start: 0.8688 (tp40) cc_final: 0.8379 (tp40) REVERT: D 50 GLN cc_start: 0.9009 (tt0) cc_final: 0.8582 (tp-100) REVERT: D 66 MET cc_start: 0.9057 (mmm) cc_final: 0.8485 (mmm) REVERT: D 324 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7565 (ptm160) REVERT: D 343 MET cc_start: 0.8500 (tpt) cc_final: 0.8150 (tpt) REVERT: D 359 PHE cc_start: 0.8543 (t80) cc_final: 0.8158 (t80) REVERT: D 380 MET cc_start: 0.8646 (mmm) cc_final: 0.8273 (mtm) REVERT: D 394 HIS cc_start: 0.8687 (m-70) cc_final: 0.8311 (t-90) REVERT: D 541 TYR cc_start: 0.8843 (m-80) cc_final: 0.8353 (m-10) REVERT: D 551 ASN cc_start: 0.9097 (t0) cc_final: 0.8746 (t0) REVERT: D 736 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (mt-10) REVERT: D 740 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7489 (tm-30) REVERT: D 744 LYS cc_start: 0.9212 (mmtm) cc_final: 0.8895 (mmtm) outliers start: 102 outliers final: 47 residues processed: 389 average time/residue: 0.5922 time to fit residues: 266.0297 Evaluate side-chains 363 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 512 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 591 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 236 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 147 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 654 ASN B 766 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.080662 restraints weight = 39590.444| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.71 r_work: 0.2899 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22700 Z= 0.136 Angle : 0.568 15.251 30740 Z= 0.286 Chirality : 0.038 0.316 3478 Planarity : 0.004 0.045 3820 Dihedral : 8.063 168.231 3266 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.26 % Allowed : 18.58 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.16), residues: 2673 helix: 2.43 (0.11), residues: 1983 sheet: None (None), residues: 0 loop : 0.18 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 324 TYR 0.019 0.001 TYR C 524 PHE 0.019 0.001 PHE D 341 TRP 0.050 0.001 TRP A 327 HIS 0.010 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (22697) covalent geometry : angle 0.56771 / 0.29 (30734) SS BOND : bond 0.00155 / 0.08 ( 3) SS BOND : angle 1.68550 / 0.79 ( 6) hydrogen bonds : bond 0.04265 / 2.82 ( 1502) hydrogen bonds : angle 3.86764 / 2.86 ( 4374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 312 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8463 (tpp) cc_final: 0.8228 (mmm) REVERT: A 81 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 102 TYR cc_start: 0.8922 (m-80) cc_final: 0.8722 (m-80) REVERT: A 136 PHE cc_start: 0.6890 (m-80) cc_final: 0.6640 (t80) REVERT: A 394 HIS cc_start: 0.7835 (m-70) cc_final: 0.7578 (m-70) REVERT: A 400 PRO cc_start: 0.8499 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8424 (mp) REVERT: A 423 TRP cc_start: 0.8208 (t-100) cc_final: 0.7387 (t60) REVERT: A 432 HIS cc_start: 0.8749 (m90) cc_final: 0.8494 (m-70) REVERT: A 492 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8006 (mtp180) REVERT: A 652 ASP cc_start: 0.8470 (t0) cc_final: 0.7451 (p0) REVERT: A 661 PHE cc_start: 0.8007 (t80) cc_final: 0.7664 (t80) REVERT: A 709 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8179 (tt0) REVERT: B 112 ASP cc_start: 0.8322 (p0) cc_final: 0.8003 (p0) REVERT: B 260 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: B 378 ARG cc_start: 0.8219 (mtt180) cc_final: 0.7976 (ptp-170) REVERT: B 425 TYR cc_start: 0.8020 (m-80) cc_final: 0.7649 (m-80) REVERT: B 443 TRP cc_start: 0.8415 (t60) cc_final: 0.7672 (t60) REVERT: B 504 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7070 (t80) REVERT: B 530 MET cc_start: 0.7772 (mtt) cc_final: 0.6752 (ttp) REVERT: B 588 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7148 (tt) REVERT: B 606 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 724 LYS cc_start: 0.8440 (ttpt) cc_final: 0.7988 (tptm) REVERT: B 727 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8100 (mtm-85) REVERT: B 729 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8829 (mm-30) REVERT: B 759 GLU cc_start: 0.8798 (tp30) cc_final: 0.8499 (tp30) REVERT: C 17 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7757 (mmm160) REVERT: C 54 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: C 118 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: C 180 GLU cc_start: 0.8414 (pp20) cc_final: 0.8159 (pp20) REVERT: C 229 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8333 (mp0) REVERT: C 286 ASP cc_start: 0.8642 (t0) cc_final: 0.7873 (t0) REVERT: C 335 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8674 (mpp) REVERT: C 416 TRP cc_start: 0.8609 (t-100) cc_final: 0.8225 (t-100) REVERT: C 421 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: C 432 HIS cc_start: 0.8752 (m-70) cc_final: 0.8508 (m-70) REVERT: C 705 ASP cc_start: 0.7917 (t0) cc_final: 0.7680 (t0) REVERT: C 711 GLN cc_start: 0.8679 (tp40) cc_final: 0.8341 (tp40) REVERT: D 50 GLN cc_start: 0.8999 (tt0) cc_final: 0.8584 (tp-100) REVERT: D 66 MET cc_start: 0.9096 (mmm) cc_final: 0.8533 (mmm) REVERT: D 324 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7584 (ptm160) REVERT: D 343 MET cc_start: 0.8454 (tpt) cc_final: 0.8145 (tpt) REVERT: D 358 LEU cc_start: 0.8887 (mt) cc_final: 0.8562 (mm) REVERT: D 359 PHE cc_start: 0.8535 (t80) cc_final: 0.8112 (t80) REVERT: D 380 MET cc_start: 0.8635 (mmm) cc_final: 0.8260 (mtm) REVERT: D 541 TYR cc_start: 0.8837 (m-80) cc_final: 0.8363 (m-10) REVERT: D 551 ASN cc_start: 0.9105 (t0) cc_final: 0.8785 (t0) REVERT: D 736 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8638 (mt-10) REVERT: D 740 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7353 (tm-30) REVERT: D 744 LYS cc_start: 0.9207 (mmtm) cc_final: 0.8826 (mmtm) outliers start: 78 outliers final: 45 residues processed: 365 average time/residue: 0.5995 time to fit residues: 252.5719 Evaluate side-chains 362 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 302 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 485 ASP Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 606 ILE Chi-restraints excluded: chain B residue 729 GLU Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 131 optimal weight: 0.6980 chunk 222 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 195 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN B 96 ASN B 535 GLN B 654 ASN B 766 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS D 177 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.113356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.081488 restraints weight = 39410.857| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.72 r_work: 0.2915 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22700 Z= 0.123 Angle : 0.571 17.804 30740 Z= 0.286 Chirality : 0.038 0.318 3478 Planarity : 0.004 0.057 3820 Dihedral : 7.902 164.871 3266 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.22 % Allowed : 19.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.16), residues: 2673 helix: 2.49 (0.11), residues: 1983 sheet: None (None), residues: 0 loop : 0.17 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 353 TYR 0.021 0.001 TYR D 430 PHE 0.020 0.001 PHE D 427 TRP 0.040 0.001 TRP C 322 HIS 0.010 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22697) covalent geometry : angle 0.57129 / 0.29 (30734) SS BOND : bond 0.00073 / 0.04 ( 3) SS BOND : angle 1.17183 / 0.49 ( 6) hydrogen bonds : bond 0.04084 / 2.70 ( 1502) hydrogen bonds : angle 3.81703 / 2.83 ( 4374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8491 (tpp) cc_final: 0.8213 (mmm) REVERT: A 81 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 102 TYR cc_start: 0.8900 (m-80) cc_final: 0.8651 (m-80) REVERT: A 286 ASP cc_start: 0.8334 (m-30) cc_final: 0.7974 (p0) REVERT: A 331 LEU cc_start: 0.9102 (mm) cc_final: 0.8605 (mm) REVERT: A 394 HIS cc_start: 0.7835 (m-70) cc_final: 0.7570 (m-70) REVERT: A 400 PRO cc_start: 0.8449 (Cg_exo) cc_final: 0.8047 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 423 TRP cc_start: 0.8208 (t-100) cc_final: 0.7397 (t60) REVERT: A 432 HIS cc_start: 0.8770 (m90) cc_final: 0.8525 (m-70) REVERT: A 492 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8016 (mtp180) REVERT: A 652 ASP cc_start: 0.8405 (t0) cc_final: 0.7380 (p0) REVERT: A 661 PHE cc_start: 0.7984 (t80) cc_final: 0.7635 (t80) REVERT: A 709 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8186 (tt0) REVERT: A 736 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 53 LEU cc_start: 0.8437 (tp) cc_final: 0.8230 (tm) REVERT: B 112 ASP cc_start: 0.8327 (p0) cc_final: 0.8026 (p0) REVERT: B 260 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: B 425 TYR cc_start: 0.8020 (m-80) cc_final: 0.7653 (m-80) REVERT: B 443 TRP cc_start: 0.8449 (t60) cc_final: 0.7693 (t60) REVERT: B 504 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.7060 (t80) REVERT: B 530 MET cc_start: 0.7703 (mtt) cc_final: 0.6738 (ttp) REVERT: B 535 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7971 (mm-40) REVERT: B 588 ILE cc_start: 0.7505 (OUTLIER) cc_final: 0.7149 (tt) REVERT: B 724 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7978 (tptm) REVERT: B 727 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8065 (mtm-85) REVERT: B 759 GLU cc_start: 0.8784 (tp30) cc_final: 0.8476 (tp30) REVERT: C 17 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7757 (mmm160) REVERT: C 54 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: C 118 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7257 (m-80) REVERT: C 174 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8634 (pp) REVERT: C 180 GLU cc_start: 0.8420 (pp20) cc_final: 0.8174 (pp20) REVERT: C 229 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: C 286 ASP cc_start: 0.8590 (t0) cc_final: 0.7828 (t0) REVERT: C 335 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8660 (mpp) REVERT: C 358 LEU cc_start: 0.9205 (mp) cc_final: 0.8924 (pp) REVERT: C 416 TRP cc_start: 0.8571 (t-100) cc_final: 0.8370 (t-100) REVERT: C 421 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: C 430 TYR cc_start: 0.8297 (t80) cc_final: 0.7236 (t80) REVERT: C 432 HIS cc_start: 0.8731 (m-70) cc_final: 0.8474 (m-70) REVERT: C 705 ASP cc_start: 0.7872 (t0) cc_final: 0.7647 (t0) REVERT: C 711 GLN cc_start: 0.8662 (tp40) cc_final: 0.8287 (tp40) REVERT: D 50 GLN cc_start: 0.8994 (tt0) cc_final: 0.8572 (tp-100) REVERT: D 66 MET cc_start: 0.9117 (mmm) cc_final: 0.8547 (mmm) REVERT: D 324 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7637 (ptm160) REVERT: D 343 MET cc_start: 0.8422 (tpt) cc_final: 0.8094 (tpt) REVERT: D 358 LEU cc_start: 0.8902 (mt) cc_final: 0.8583 (mm) REVERT: D 359 PHE cc_start: 0.8515 (t80) cc_final: 0.8083 (t80) REVERT: D 380 MET cc_start: 0.8627 (mmm) cc_final: 0.8272 (mtm) REVERT: D 422 MET cc_start: 0.8605 (mmm) cc_final: 0.8339 (mmp) REVERT: D 541 TYR cc_start: 0.8820 (m-80) cc_final: 0.8332 (m-10) REVERT: D 551 ASN cc_start: 0.9100 (t0) cc_final: 0.8800 (t0) REVERT: D 736 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: D 740 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7314 (tm-30) REVERT: D 744 LYS cc_start: 0.9173 (mmtm) cc_final: 0.8889 (mmtm) outliers start: 77 outliers final: 32 residues processed: 379 average time/residue: 0.5345 time to fit residues: 235.1045 Evaluate side-chains 360 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 119 optimal weight: 0.0010 chunk 112 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 169 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 535 GLN B 654 ASN B 766 GLN ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082935 restraints weight = 39558.475| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.72 r_work: 0.2986 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22700 Z= 0.128 Angle : 0.605 17.910 30740 Z= 0.301 Chirality : 0.039 0.378 3478 Planarity : 0.004 0.059 3820 Dihedral : 7.800 162.384 3264 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.59 % Allowed : 20.08 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.16), residues: 2673 helix: 2.47 (0.11), residues: 1982 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 353 TYR 0.028 0.001 TYR D 348 PHE 0.052 0.001 PHE B 483 TRP 0.045 0.001 TRP A 327 HIS 0.019 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (22697) covalent geometry : angle 0.60446 / 0.30 (30734) SS BOND : bond 0.00072 / 0.04 ( 3) SS BOND : angle 1.05734 / 0.46 ( 6) hydrogen bonds : bond 0.04082 / 2.70 ( 1502) hydrogen bonds : angle 3.82454 / 2.84 ( 4374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 318 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8660 (tt0) cc_final: 0.8352 (mt-10) REVERT: A 66 MET cc_start: 0.8502 (tpp) cc_final: 0.8209 (mmm) REVERT: A 81 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8297 (mt-10) REVERT: A 102 TYR cc_start: 0.8857 (m-80) cc_final: 0.8598 (m-80) REVERT: A 331 LEU cc_start: 0.8867 (mm) cc_final: 0.8596 (mp) REVERT: A 394 HIS cc_start: 0.7853 (m-70) cc_final: 0.7589 (m-70) REVERT: A 400 PRO cc_start: 0.8424 (Cg_exo) cc_final: 0.8076 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 423 TRP cc_start: 0.8222 (t-100) cc_final: 0.7442 (t60) REVERT: A 432 HIS cc_start: 0.8774 (m170) cc_final: 0.8516 (m-70) REVERT: A 468 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8751 (tt0) REVERT: A 492 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8053 (mtp180) REVERT: A 652 ASP cc_start: 0.8355 (t0) cc_final: 0.7375 (p0) REVERT: A 661 PHE cc_start: 0.8006 (t80) cc_final: 0.7697 (t80) REVERT: A 709 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8232 (tt0) REVERT: A 736 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 53 LEU cc_start: 0.8421 (tp) cc_final: 0.8167 (tm) REVERT: B 112 ASP cc_start: 0.8323 (p0) cc_final: 0.8024 (p0) REVERT: B 204 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9170 (tttp) REVERT: B 305 MET cc_start: 0.6938 (mmp) cc_final: 0.6399 (mmp) REVERT: B 425 TYR cc_start: 0.8048 (m-80) cc_final: 0.7700 (m-80) REVERT: B 443 TRP cc_start: 0.8440 (t60) cc_final: 0.7690 (t60) REVERT: B 485 ASP cc_start: 0.8198 (t70) cc_final: 0.7841 (p0) REVERT: B 504 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 530 MET cc_start: 0.7623 (mtt) cc_final: 0.6725 (ttp) REVERT: B 549 PHE cc_start: 0.7673 (m-10) cc_final: 0.7081 (t80) REVERT: B 588 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7204 (tt) REVERT: B 724 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7995 (tptm) REVERT: B 727 ARG cc_start: 0.8348 (mtp85) cc_final: 0.8033 (mtm-85) REVERT: C 17 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7700 (mmm160) REVERT: C 54 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: C 118 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: C 174 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8633 (pp) REVERT: C 180 GLU cc_start: 0.8435 (pp20) cc_final: 0.8175 (pp20) REVERT: C 229 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: C 286 ASP cc_start: 0.8566 (t0) cc_final: 0.7786 (t0) REVERT: C 335 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8655 (mpp) REVERT: C 358 LEU cc_start: 0.9222 (mp) cc_final: 0.8933 (pp) REVERT: C 416 TRP cc_start: 0.8590 (t-100) cc_final: 0.8375 (t-100) REVERT: C 421 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7629 (pt0) REVERT: C 430 TYR cc_start: 0.8323 (t80) cc_final: 0.7316 (t80) REVERT: C 432 HIS cc_start: 0.8717 (m-70) cc_final: 0.8466 (m-70) REVERT: C 705 ASP cc_start: 0.7831 (t0) cc_final: 0.7609 (t0) REVERT: C 711 GLN cc_start: 0.8636 (tp40) cc_final: 0.8249 (tp40) REVERT: D 50 GLN cc_start: 0.9001 (tt0) cc_final: 0.8601 (tp-100) REVERT: D 66 MET cc_start: 0.9112 (mmm) cc_final: 0.8563 (mmm) REVERT: D 324 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7638 (ptm160) REVERT: D 331 LEU cc_start: 0.9042 (tt) cc_final: 0.8640 (tp) REVERT: D 335 MET cc_start: 0.9221 (mmm) cc_final: 0.8906 (mpp) REVERT: D 343 MET cc_start: 0.8455 (tpt) cc_final: 0.8108 (tpt) REVERT: D 359 PHE cc_start: 0.8433 (t80) cc_final: 0.7957 (t80) REVERT: D 380 MET cc_start: 0.8662 (mmm) cc_final: 0.8317 (mtm) REVERT: D 541 TYR cc_start: 0.8821 (m-80) cc_final: 0.8344 (m-10) REVERT: D 551 ASN cc_start: 0.9107 (t0) cc_final: 0.8816 (t0) REVERT: D 736 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: D 740 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7292 (tm-30) REVERT: D 744 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8913 (mmtm) outliers start: 62 outliers final: 31 residues processed: 361 average time/residue: 0.5409 time to fit residues: 226.8987 Evaluate side-chains 350 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 305 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 188 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 0.0970 chunk 112 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 244 optimal weight: 0.1980 chunk 217 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 535 GLN B 654 ASN B 766 GLN ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 177 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.115291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084105 restraints weight = 39465.832| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.73 r_work: 0.3004 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22700 Z= 0.120 Angle : 0.599 17.524 30740 Z= 0.299 Chirality : 0.038 0.421 3478 Planarity : 0.004 0.060 3820 Dihedral : 7.659 156.848 3264 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.88 % Allowed : 21.04 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.16), residues: 2673 helix: 2.50 (0.11), residues: 1985 sheet: None (None), residues: 0 loop : 0.15 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 353 TYR 0.022 0.001 TYR D 348 PHE 0.021 0.001 PHE D 341 TRP 0.039 0.001 TRP C 322 HIS 0.014 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22697) covalent geometry : angle 0.59911 / 0.30 (30734) SS BOND : bond 0.00092 / 0.05 ( 3) SS BOND : angle 0.95862 / 0.45 ( 6) hydrogen bonds : bond 0.03928 / 2.61 ( 1502) hydrogen bonds : angle 3.81642 / 2.82 ( 4374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 328 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8631 (tt0) cc_final: 0.8346 (mt-10) REVERT: A 66 MET cc_start: 0.8519 (tpp) cc_final: 0.8204 (mmm) REVERT: A 81 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 102 TYR cc_start: 0.8831 (m-80) cc_final: 0.8586 (m-80) REVERT: A 286 ASP cc_start: 0.8313 (m-30) cc_final: 0.7984 (p0) REVERT: A 394 HIS cc_start: 0.7862 (m-70) cc_final: 0.7604 (m-70) REVERT: A 400 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8004 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 423 TRP cc_start: 0.8224 (t-100) cc_final: 0.7446 (t60) REVERT: A 432 HIS cc_start: 0.8764 (m170) cc_final: 0.8524 (m-70) REVERT: A 468 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8774 (tt0) REVERT: A 492 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: A 652 ASP cc_start: 0.8300 (t0) cc_final: 0.7359 (p0) REVERT: A 661 PHE cc_start: 0.7990 (t80) cc_final: 0.7735 (t80) REVERT: A 709 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8192 (pt0) REVERT: A 733 LYS cc_start: 0.8619 (mttm) cc_final: 0.8385 (mtmt) REVERT: A 736 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 53 LEU cc_start: 0.8432 (tp) cc_final: 0.8172 (tm) REVERT: B 112 ASP cc_start: 0.8330 (p0) cc_final: 0.8034 (p0) REVERT: B 305 MET cc_start: 0.6945 (mmp) cc_final: 0.6395 (mmp) REVERT: B 425 TYR cc_start: 0.8048 (m-80) cc_final: 0.7701 (m-80) REVERT: B 443 TRP cc_start: 0.8436 (t60) cc_final: 0.7681 (t60) REVERT: B 485 ASP cc_start: 0.8259 (t70) cc_final: 0.7948 (p0) REVERT: B 487 LYS cc_start: 0.8855 (pptt) cc_final: 0.8531 (pptt) REVERT: B 504 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 530 MET cc_start: 0.7727 (mtt) cc_final: 0.6723 (ttp) REVERT: B 535 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: B 549 PHE cc_start: 0.7627 (m-10) cc_final: 0.7040 (t80) REVERT: B 588 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7222 (tt) REVERT: B 724 LYS cc_start: 0.8421 (ttpt) cc_final: 0.8033 (tptm) REVERT: B 727 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8011 (mtm-85) REVERT: C 17 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7675 (mmm160) REVERT: C 54 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: C 118 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: C 174 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8617 (pp) REVERT: C 180 GLU cc_start: 0.8446 (pp20) cc_final: 0.8196 (pp20) REVERT: C 229 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: C 240 GLU cc_start: 0.8869 (mp0) cc_final: 0.8569 (mp0) REVERT: C 286 ASP cc_start: 0.8598 (t0) cc_final: 0.7880 (t0) REVERT: C 324 ARG cc_start: 0.7339 (mpp-170) cc_final: 0.7112 (mmt180) REVERT: C 335 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8643 (mpp) REVERT: C 358 LEU cc_start: 0.9228 (mp) cc_final: 0.8943 (pp) REVERT: C 416 TRP cc_start: 0.8558 (t-100) cc_final: 0.8192 (t-100) REVERT: C 421 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7839 (pt0) REVERT: C 432 HIS cc_start: 0.8670 (m-70) cc_final: 0.8410 (m-70) REVERT: C 711 GLN cc_start: 0.8616 (tp40) cc_final: 0.8218 (tp40) REVERT: D 50 GLN cc_start: 0.9003 (tt0) cc_final: 0.8589 (tp-100) REVERT: D 66 MET cc_start: 0.9126 (mmm) cc_final: 0.8613 (mmm) REVERT: D 324 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7654 (ptm160) REVERT: D 331 LEU cc_start: 0.9079 (tt) cc_final: 0.8704 (tp) REVERT: D 335 MET cc_start: 0.9173 (mmm) cc_final: 0.8947 (mpp) REVERT: D 343 MET cc_start: 0.8461 (tpt) cc_final: 0.8131 (tpt) REVERT: D 358 LEU cc_start: 0.8877 (mt) cc_final: 0.8570 (mm) REVERT: D 359 PHE cc_start: 0.8376 (t80) cc_final: 0.7783 (t80) REVERT: D 380 MET cc_start: 0.8662 (mmm) cc_final: 0.8326 (mtm) REVERT: D 422 MET cc_start: 0.8721 (mmt) cc_final: 0.8513 (mmm) REVERT: D 541 TYR cc_start: 0.8798 (m-80) cc_final: 0.8328 (m-10) REVERT: D 551 ASN cc_start: 0.9101 (t0) cc_final: 0.8821 (t0) REVERT: D 740 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7324 (tm-30) REVERT: D 744 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8922 (mmtm) outliers start: 45 outliers final: 23 residues processed: 358 average time/residue: 0.5389 time to fit residues: 222.7644 Evaluate side-chains 343 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 703 HIS Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 504 PHE Chi-restraints excluded: chain B residue 535 GLN Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain C residue 17 ARG Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 324 ARG Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 250 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 244 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 535 GLN B 766 GLN C 432 HIS ** C 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.081605 restraints weight = 39942.383| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.70 r_work: 0.2984 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22700 Z= 0.140 Angle : 0.615 17.064 30740 Z= 0.308 Chirality : 0.039 0.402 3478 Planarity : 0.004 0.052 3820 Dihedral : 7.659 151.799 3264 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.73 % Favored : 97.23 % Rotamer: Outliers : 1.88 % Allowed : 21.25 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.16), residues: 2673 helix: 2.44 (0.11), residues: 1985 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 545 TYR 0.019 0.001 TYR C 524 PHE 0.020 0.001 PHE D 341 TRP 0.045 0.001 TRP A 327 HIS 0.015 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (22697) covalent geometry : angle 0.61479 / 0.31 (30734) SS BOND : bond 0.00088 / 0.04 ( 3) SS BOND : angle 1.02874 / 0.45 ( 6) hydrogen bonds : bond 0.04143 / 2.73 ( 1502) hydrogen bonds : angle 3.86834 / 2.86 ( 4374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7257.11 seconds wall clock time: 124 minutes 45.77 seconds (7485.77 seconds total)