Starting phenix.real_space_refine on Fri Feb 6 04:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4i_62060/02_2026/9k4i_62060.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4i_62060/02_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_62060/02_2026/9k4i_62060.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4i_62060/02_2026/9k4i_62060.map" model { file = "/net/cci-nas-00/data/ceres_data/9k4i_62060/02_2026/9k4i_62060.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4i_62060/02_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-2.0-5952/lib/python3.9/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, 75 Unusual residues: {' CA': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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, 114 Unusual residues: {' CA': 1, 'Y01': 1, 'YZY': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 36 Unusual residues: {' CA': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.57, per 1000 atoms: 0.25 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: 1.96 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.69 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: 4.25 Time building geometry restraints manager: 2.68 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 2.510 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: 6.320 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.090 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 covalent geometry : bond 0.01002 (22697) covalent geometry : angle 1.10465 (30734) SS BOND : bond 0.00246 ( 3) SS BOND : angle 0.45900 ( 6) hydrogen bonds : bond 0.18440 ( 1502) hydrogen bonds : angle 7.11995 ( 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 : 0.975 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: 0.8323 (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: 0.6587 time to fit residues: 462.3547 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 : 0.912 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3675 r_free = 0.3675 target = 0.116016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084920 restraints weight = 38860.068| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.65 r_work: 0.2967 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22700 Z= 0.142 Angle : 0.566 10.768 30740 Z= 0.297 Chirality : 0.039 0.361 3478 Planarity : 0.004 0.047 3820 Dihedral : 11.724 179.666 3272 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.09 % Allowed : 12.86 % Favored : 84.05 % 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: 2.34 (0.16), residues: 2673 helix: 2.17 (0.11), residues: 1965 sheet: None (None), residues: 0 loop : -0.20 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.019 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00300 (22697) covalent geometry : angle 0.56643 (30734) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.69522 ( 6) hydrogen bonds : bond 0.05240 ( 1502) hydrogen bonds : angle 4.39889 ( 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 483 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 409 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.8576 (t70) cc_final: 0.8368 (t0) REVERT: A 81 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8157 (mt-10) REVERT: A 102 TYR cc_start: 0.8507 (m-80) cc_final: 0.8067 (m-80) REVERT: A 238 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8427 (ttmp) REVERT: A 327 TRP cc_start: 0.8839 (p-90) cc_final: 0.8453 (p-90) REVERT: A 339 PHE cc_start: 0.9073 (m-80) cc_final: 0.8791 (m-80) REVERT: A 394 HIS cc_start: 0.7551 (m-70) cc_final: 0.7264 (m-70) REVERT: A 400 PRO cc_start: 0.8537 (Cg_exo) cc_final: 0.8202 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8360 (t-100) cc_final: 0.7551 (t60) REVERT: A 512 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7419 (mmp-170) REVERT: A 629 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: A 709 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8078 (pt0) REVERT: A 738 LEU cc_start: 0.8890 (mt) cc_final: 0.8656 (mp) REVERT: B 53 LEU cc_start: 0.8275 (tp) cc_final: 0.8050 (tm) REVERT: B 112 ASP cc_start: 0.8429 (p0) cc_final: 0.8055 (p0) REVERT: B 504 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 530 MET cc_start: 0.7680 (mtt) cc_final: 0.6459 (tmt) REVERT: B 606 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8294 (mt) REVERT: B 654 ASN cc_start: 0.8791 (m-40) cc_final: 0.8582 (m-40) REVERT: B 724 LYS cc_start: 0.8485 (ttpt) cc_final: 0.7826 (tptt) REVERT: B 727 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7742 (ptp-170) REVERT: C 17 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7693 (mmm160) REVERT: C 32 GLU cc_start: 0.8845 (mp0) cc_final: 0.8548 (pm20) REVERT: C 118 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.6978 (m-80) REVERT: C 174 ILE cc_start: 0.8705 (pp) cc_final: 0.8432 (mp) REVERT: C 229 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: C 247 GLN cc_start: 0.9141 (tt0) cc_final: 0.8898 (tt0) REVERT: C 286 ASP cc_start: 0.8417 (t0) cc_final: 0.7723 (t0) REVERT: C 331 LEU cc_start: 0.8940 (tp) cc_final: 0.8722 (tp) REVERT: C 335 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8917 (mpp) REVERT: C 339 PHE cc_start: 0.9062 (m-80) cc_final: 0.8859 (t80) REVERT: C 430 TYR cc_start: 0.8177 (t80) cc_final: 0.7852 (t80) REVERT: C 432 HIS cc_start: 0.8482 (m90) cc_final: 0.8256 (m-70) REVERT: C 450 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7925 (mm) REVERT: C 491 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8099 (mp) REVERT: C 595 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: C 636 ASP cc_start: 0.9018 (m-30) cc_final: 0.8719 (p0) REVERT: C 711 GLN cc_start: 0.8609 (tp40) cc_final: 0.8348 (tp40) REVERT: D 50 GLN cc_start: 0.8943 (tt0) cc_final: 0.8474 (tp40) REVERT: D 66 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8720 (mmt) REVERT: D 177 ASN cc_start: 0.9167 (p0) cc_final: 0.8957 (p0) REVERT: D 343 MET cc_start: 0.8420 (tpt) cc_final: 0.8073 (tpt) REVERT: D 358 LEU cc_start: 0.8983 (mt) cc_final: 0.8685 (mm) REVERT: D 394 HIS cc_start: 0.7938 (m-70) cc_final: 0.7666 (m-70) REVERT: D 657 LEU cc_start: 0.8390 (mp) cc_final: 0.8164 (mp) REVERT: D 744 LYS cc_start: 0.9072 (mmtm) cc_final: 0.8740 (mmtm) outliers start: 74 outliers final: 13 residues processed: 452 average time/residue: 0.5871 time to fit residues: 304.1816 Evaluate side-chains 344 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 318 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 335 MET 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: 3.9990 chunk 213 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 206 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 308 GLN A 432 HIS A 634 HIS A 748 GLN B 766 GLN C 629 GLN C 748 GLN D 82 ASN D 192 HIS D 306 ASN D 625 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.112417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080805 restraints weight = 39588.004| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.69 r_work: 0.2893 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22700 Z= 0.168 Angle : 0.554 8.517 30740 Z= 0.289 Chirality : 0.038 0.311 3478 Planarity : 0.004 0.073 3820 Dihedral : 10.269 178.820 3266 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.26 % Allowed : 14.70 % Favored : 81.04 % 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: 2.78 (0.16), residues: 2673 helix: 2.42 (0.11), residues: 1961 sheet: None (None), residues: 0 loop : 0.22 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 211 TYR 0.015 0.001 TYR C 460 PHE 0.018 0.002 PHE B 544 TRP 0.025 0.001 TRP A 327 HIS 0.014 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00387 (22697) covalent geometry : angle 0.55381 (30734) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.53528 ( 6) hydrogen bonds : bond 0.04964 ( 1502) hydrogen bonds : angle 4.12708 ( 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 451 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 349 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 102 TYR cc_start: 0.8775 (m-80) cc_final: 0.8523 (m-80) REVERT: A 327 TRP cc_start: 0.8696 (p-90) cc_final: 0.8391 (p-90) REVERT: A 400 PRO cc_start: 0.8540 (Cg_exo) cc_final: 0.8193 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8372 (mp) REVERT: A 423 TRP cc_start: 0.8299 (t-100) cc_final: 0.7434 (t60) REVERT: A 432 HIS cc_start: 0.8637 (m90) cc_final: 0.8436 (m-70) REVERT: A 529 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8918 (tp) REVERT: A 629 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7577 (mp-120) REVERT: A 709 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8007 (pt0) REVERT: A 733 LYS cc_start: 0.8677 (mttm) cc_final: 0.8424 (mtmt) REVERT: A 748 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: B 53 LEU cc_start: 0.8431 (tp) cc_final: 0.8204 (tm) REVERT: B 112 ASP cc_start: 0.8387 (p0) cc_final: 0.8013 (p0) REVERT: B 260 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 425 TYR cc_start: 0.7864 (m-80) cc_final: 0.7593 (m-80) REVERT: B 504 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6928 (t80) REVERT: B 530 MET cc_start: 0.7927 (mtt) cc_final: 0.6748 (pp-130) REVERT: B 606 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8395 (mt) REVERT: B 724 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8043 (tptt) REVERT: B 727 ARG cc_start: 0.8417 (mtp85) cc_final: 0.8181 (mtm-85) REVERT: B 759 GLU cc_start: 0.8546 (tp30) cc_final: 0.8329 (tp30) REVERT: C 17 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7804 (mmm160) REVERT: C 118 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7082 (m-80) REVERT: C 229 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: C 286 ASP cc_start: 0.8591 (t0) cc_final: 0.7812 (t0) REVERT: C 335 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8784 (mpp) REVERT: C 421 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7732 (pt0) REVERT: C 450 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7969 (mm) REVERT: C 513 MET cc_start: 0.8043 (mtm) cc_final: 0.7619 (mtm) REVERT: C 711 GLN cc_start: 0.8681 (tp40) cc_final: 0.8330 (tp40) REVERT: D 50 GLN cc_start: 0.8985 (tt0) cc_final: 0.8533 (tp-100) REVERT: D 343 MET cc_start: 0.8426 (tpt) cc_final: 0.8078 (tpt) REVERT: D 359 PHE cc_start: 0.8587 (t80) cc_final: 0.8196 (t80) REVERT: D 541 TYR cc_start: 0.8807 (m-80) cc_final: 0.8252 (m-10) REVERT: D 551 ASN cc_start: 0.9018 (t0) cc_final: 0.8658 (t0) REVERT: D 657 LEU cc_start: 0.8266 (mp) cc_final: 0.8043 (mp) REVERT: D 736 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8657 (mt-10) REVERT: D 740 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 744 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8984 (mmtm) outliers start: 102 outliers final: 28 residues processed: 418 average time/residue: 0.5744 time to fit residues: 276.8984 Evaluate side-chains 354 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 419 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 634 HIS 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 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 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 18 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL 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: 2.9990 chunk 203 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 748 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.111669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079733 restraints weight = 39543.045| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.69 r_work: 0.2881 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22700 Z= 0.166 Angle : 0.566 15.226 30740 Z= 0.290 Chirality : 0.039 0.321 3478 Planarity : 0.004 0.071 3820 Dihedral : 9.380 175.443 3266 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.01 % Allowed : 15.53 % Favored : 80.46 % 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: 2.82 (0.16), residues: 2673 helix: 2.43 (0.11), residues: 1961 sheet: None (None), residues: 0 loop : 0.34 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 255 TYR 0.018 0.001 TYR D 430 PHE 0.018 0.001 PHE B 544 TRP 0.017 0.001 TRP A 327 HIS 0.021 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00388 (22697) covalent geometry : angle 0.56562 (30734) SS BOND : bond 0.00186 ( 3) SS BOND : angle 0.36286 ( 6) hydrogen bonds : bond 0.04753 ( 1502) hydrogen bonds : angle 4.04303 ( 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 434 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 338 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8534 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 102 TYR cc_start: 0.8824 (m-80) cc_final: 0.8590 (m-80) REVERT: A 327 TRP cc_start: 0.8741 (p-90) cc_final: 0.8518 (p-90) REVERT: A 350 ILE cc_start: 0.8625 (mt) cc_final: 0.8416 (pt) REVERT: A 394 HIS cc_start: 0.7711 (m-70) cc_final: 0.7466 (m-70) REVERT: A 400 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8213 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8312 (t-100) cc_final: 0.7474 (t60) REVERT: A 512 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7454 (mmp-170) REVERT: A 629 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7546 (mp-120) REVERT: A 709 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8099 (tt0) REVERT: B 53 LEU cc_start: 0.8367 (tp) cc_final: 0.8130 (tm) REVERT: B 112 ASP cc_start: 0.8367 (p0) cc_final: 0.8022 (p0) REVERT: B 260 GLU cc_start: 0.8627 (mp0) cc_final: 0.8342 (mp0) REVERT: B 425 TYR cc_start: 0.7964 (m-80) cc_final: 0.7649 (m-80) REVERT: B 504 PHE cc_start: 0.7519 (OUTLIER) cc_final: 0.7029 (t80) REVERT: B 530 MET cc_start: 0.7900 (mtt) cc_final: 0.6741 (ttp) REVERT: B 606 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (mt) REVERT: B 724 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8117 (tptt) REVERT: B 727 ARG cc_start: 0.8443 (mtp85) cc_final: 0.8182 (mtm-85) REVERT: B 729 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8819 (mm-30) REVERT: B 759 GLU cc_start: 0.8607 (tp30) cc_final: 0.8367 (tp30) REVERT: C 17 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7784 (mmm160) REVERT: C 54 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: C 118 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: C 286 ASP cc_start: 0.8583 (t0) cc_final: 0.7815 (t0) REVERT: C 335 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8823 (mpp) REVERT: C 421 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: C 595 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: C 711 GLN cc_start: 0.8687 (tp40) cc_final: 0.8331 (tp40) REVERT: D 50 GLN cc_start: 0.8986 (tt0) cc_final: 0.8590 (tp40) REVERT: D 66 MET cc_start: 0.8959 (mmm) cc_final: 0.8304 (mmm) REVERT: D 343 MET cc_start: 0.8409 (tpt) cc_final: 0.8089 (tpt) REVERT: D 359 PHE cc_start: 0.8607 (t80) cc_final: 0.8236 (t80) REVERT: D 380 MET cc_start: 0.8609 (mmm) cc_final: 0.8261 (mtm) REVERT: D 465 PRO cc_start: 0.8890 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: D 512 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8350 (tpm170) REVERT: D 541 TYR cc_start: 0.8796 (m-80) cc_final: 0.8252 (m-10) REVERT: D 551 ASN cc_start: 0.9046 (t0) cc_final: 0.8683 (t0) REVERT: D 736 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8646 (mt-10) REVERT: D 740 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7562 (tm-30) REVERT: D 744 LYS cc_start: 0.9199 (mmtm) cc_final: 0.8860 (mmtm) outliers start: 96 outliers final: 38 residues processed: 396 average time/residue: 0.6166 time to fit residues: 279.7884 Evaluate side-chains 368 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 317 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 118 TYR Chi-restraints excluded: chain C residue 186 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 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 759 ASP Chi-restraints excluded: chain D residue 18 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 262 SER 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 444 SER 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 617 LEU Chi-restraints excluded: chain D residue 634 HIS Chi-restraints excluded: chain D residue 652 ASP Chi-restraints excluded: chain D residue 703 HIS Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 738 LEU Chi-restraints excluded: chain D residue 759 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 5 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 177 optimal weight: 0.1980 chunk 156 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 256 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS B 96 ASN B 766 GLN C 629 GLN C 742 ASN C 748 GLN D 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.113769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082060 restraints weight = 39299.059| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.69 r_work: 0.2926 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4478 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= 0.118 Angle : 0.531 13.991 30740 Z= 0.273 Chirality : 0.037 0.321 3478 Planarity : 0.004 0.065 3820 Dihedral : 8.518 171.964 3266 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.84 % Allowed : 16.83 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.94 (0.16), residues: 2673 helix: 2.50 (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 0.018 0.001 TYR C 446 PHE 0.016 0.001 PHE D 520 TRP 0.020 0.001 TRP C 322 HIS 0.017 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00256 (22697) covalent geometry : angle 0.53057 (30734) SS BOND : bond 0.00185 ( 3) SS BOND : angle 0.43906 ( 6) hydrogen bonds : bond 0.04184 ( 1502) hydrogen bonds : angle 3.88924 ( 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 437 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 345 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 102 TYR cc_start: 0.8793 (m-80) cc_final: 0.7710 (m-80) REVERT: A 327 TRP cc_start: 0.8703 (p-90) cc_final: 0.8460 (p-90) REVERT: A 394 HIS cc_start: 0.7790 (m-70) cc_final: 0.7534 (m-70) REVERT: A 400 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8148 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8242 (t-100) cc_final: 0.7382 (t60) REVERT: A 512 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7380 (mmp-170) REVERT: A 629 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7421 (mp-120) REVERT: A 709 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8103 (pt0) REVERT: B 53 LEU cc_start: 0.8309 (tp) cc_final: 0.8083 (tm) REVERT: B 112 ASP cc_start: 0.8325 (p0) cc_final: 0.7971 (p0) REVERT: B 260 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: B 425 TYR cc_start: 0.7998 (m-80) cc_final: 0.7606 (m-80) REVERT: B 504 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7052 (t80) REVERT: B 530 MET cc_start: 0.7776 (mtt) cc_final: 0.6696 (ttp) REVERT: B 606 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 724 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8016 (tptt) REVERT: B 727 ARG cc_start: 0.8408 (mtp85) cc_final: 0.8138 (mtm-85) REVERT: B 729 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8823 (mm-30) REVERT: B 759 GLU cc_start: 0.8674 (tp30) cc_final: 0.8444 (tp30) REVERT: C 17 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7771 (mmm160) REVERT: C 54 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: C 118 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.7188 (m-80) REVERT: C 286 ASP cc_start: 0.8582 (t0) cc_final: 0.7780 (t0) REVERT: C 335 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8687 (mpp) REVERT: C 421 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7880 (pt0) REVERT: C 430 TYR cc_start: 0.8330 (t80) cc_final: 0.8010 (t80) REVERT: C 432 HIS cc_start: 0.8702 (m-70) cc_final: 0.8443 (m-70) REVERT: C 661 PHE cc_start: 0.7661 (t80) cc_final: 0.7329 (t80) REVERT: C 705 ASP cc_start: 0.7902 (t0) cc_final: 0.7626 (t0) REVERT: C 711 GLN cc_start: 0.8638 (tp40) cc_final: 0.8258 (tp40) REVERT: D 50 GLN cc_start: 0.8974 (tt0) cc_final: 0.8550 (tp-100) REVERT: D 66 MET cc_start: 0.9038 (mmm) cc_final: 0.8496 (mmm) REVERT: D 81 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8599 (mt-10) REVERT: D 343 MET cc_start: 0.8418 (tpt) cc_final: 0.8093 (tpt) REVERT: D 358 LEU cc_start: 0.8960 (mt) cc_final: 0.8650 (mm) REVERT: D 359 PHE cc_start: 0.8487 (t80) cc_final: 0.8060 (t80) REVERT: D 380 MET cc_start: 0.8584 (mmm) cc_final: 0.8281 (mtm) REVERT: D 465 PRO cc_start: 0.8734 (Cg_exo) cc_final: 0.8495 (Cg_endo) REVERT: D 512 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8167 (tpm170) REVERT: D 541 TYR cc_start: 0.8775 (m-80) cc_final: 0.8287 (m-10) REVERT: D 652 ASP cc_start: 0.8593 (t0) cc_final: 0.8301 (OUTLIER) REVERT: D 736 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8650 (mt-10) REVERT: D 740 GLU cc_start: 0.8247 (tm-30) cc_final: 0.7377 (tm-30) REVERT: D 744 LYS cc_start: 0.9189 (mmtm) cc_final: 0.8863 (mmtm) outliers start: 92 outliers final: 33 residues processed: 405 average time/residue: 0.6031 time to fit residues: 281.2422 Evaluate side-chains 353 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 308 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE 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 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 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 462 MET 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 54 GLU 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 C residue 442 MET Chi-restraints excluded: chain C residue 553 CYS 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 512 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 17 optimal weight: 0.8980 chunk 219 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 173 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 162 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS B 96 ASN B 654 ASN B 766 GLN C 247 GLN C 629 GLN C 735 ASN C 748 GLN D 177 ASN D 709 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.110882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078535 restraints weight = 39408.557| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.72 r_work: 0.2869 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22700 Z= 0.177 Angle : 0.581 14.739 30740 Z= 0.294 Chirality : 0.039 0.318 3478 Planarity : 0.004 0.061 3820 Dihedral : 8.356 170.474 3266 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.72 % Allowed : 17.70 % Favored : 78.58 % 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: 2.83 (0.16), residues: 2673 helix: 2.42 (0.11), residues: 1965 sheet: None (None), residues: 0 loop : 0.35 (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 D 430 PHE 0.019 0.002 PHE C 319 TRP 0.022 0.001 TRP C 322 HIS 0.026 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00417 (22697) covalent geometry : angle 0.58076 (30734) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.96819 ( 6) hydrogen bonds : bond 0.04631 ( 1502) hydrogen bonds : angle 3.95697 ( 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 415 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 326 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 394 HIS cc_start: 0.7775 (m-70) cc_final: 0.7513 (m-70) REVERT: A 400 PRO cc_start: 0.8557 (Cg_exo) cc_final: 0.8187 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 423 TRP cc_start: 0.8285 (t-100) cc_final: 0.7456 (t60) REVERT: A 492 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8048 (mtp180) REVERT: A 512 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7471 (mmp-170) REVERT: A 629 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7453 (mp-120) REVERT: A 709 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8121 (tt0) REVERT: B 53 LEU cc_start: 0.8345 (tp) cc_final: 0.8091 (tm) REVERT: B 112 ASP cc_start: 0.8340 (p0) cc_final: 0.8014 (p0) REVERT: B 260 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: B 425 TYR cc_start: 0.7999 (m-80) cc_final: 0.7661 (m-80) REVERT: B 504 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7104 (t80) REVERT: B 530 MET cc_start: 0.7982 (mtt) cc_final: 0.6737 (tmm) REVERT: B 588 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.7158 (tt) REVERT: B 606 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 724 LYS cc_start: 0.8425 (ttpt) cc_final: 0.7965 (tptm) REVERT: B 727 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8169 (mtm-85) REVERT: B 729 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (mm-30) REVERT: B 759 GLU cc_start: 0.8756 (tp30) cc_final: 0.8493 (tp30) REVERT: C 17 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7780 (mmm160) REVERT: C 54 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8297 (mt-10) REVERT: C 118 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: C 240 GLU cc_start: 0.8872 (mp0) cc_final: 0.8647 (mp0) REVERT: C 286 ASP cc_start: 0.8612 (t0) cc_final: 0.7847 (t0) REVERT: C 335 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8693 (mpp) REVERT: C 406 MET cc_start: 0.8677 (mtp) cc_final: 0.8210 (mtt) REVERT: C 410 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7595 (m-90) REVERT: C 421 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7789 (pt0) REVERT: C 432 HIS cc_start: 0.8730 (m-70) cc_final: 0.8416 (m-70) REVERT: C 518 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 705 ASP cc_start: 0.7948 (t0) cc_final: 0.7677 (t0) REVERT: C 711 GLN cc_start: 0.8717 (tp40) cc_final: 0.8410 (tp40) REVERT: D 50 GLN cc_start: 0.9002 (tt0) cc_final: 0.8591 (tp40) REVERT: D 66 MET cc_start: 0.9080 (mmm) cc_final: 0.8480 (mmm) REVERT: D 343 MET cc_start: 0.8478 (tpt) cc_final: 0.8162 (tpt) REVERT: D 359 PHE cc_start: 0.8566 (t80) cc_final: 0.8190 (t80) REVERT: D 465 PRO cc_start: 0.8715 (Cg_exo) cc_final: 0.8448 (Cg_endo) REVERT: D 541 TYR cc_start: 0.8780 (m-80) cc_final: 0.8235 (m-10) REVERT: D 551 ASN cc_start: 0.9109 (t0) cc_final: 0.8769 (t0) REVERT: D 559 GLU cc_start: 0.8583 (tt0) cc_final: 0.8239 (tp30) REVERT: D 652 ASP cc_start: 0.8612 (t0) cc_final: 0.8310 (t0) REVERT: D 736 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: D 740 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7540 (tm-30) REVERT: D 744 LYS cc_start: 0.9206 (mmtm) cc_final: 0.8896 (mmtm) outliers start: 89 outliers final: 42 residues processed: 385 average time/residue: 0.5759 time to fit residues: 255.2243 Evaluate side-chains 363 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 304 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 108 VAL Chi-restraints excluded: chain A residue 182 VAL 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 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 738 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 504 PHE Chi-restraints excluded: chain B residue 523 LEU 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 54 GLU 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 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 410 TRP Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU 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 262 SER 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 444 SER Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 513 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 236 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 0.0170 chunk 121 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 ASN B 654 ASN B 766 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** 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 = 0.3616 r_free = 0.3616 target = 0.111693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079731 restraints weight = 39623.307| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.71 r_work: 0.2883 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22700 Z= 0.151 Angle : 0.579 17.391 30740 Z= 0.292 Chirality : 0.038 0.342 3478 Planarity : 0.004 0.057 3820 Dihedral : 8.188 169.494 3266 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.47 % Allowed : 18.62 % Favored : 77.91 % 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: 2.74 (0.16), residues: 2673 helix: 2.36 (0.11), residues: 1986 sheet: None (None), residues: 0 loop : 0.24 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 324 TYR 0.020 0.001 TYR C 524 PHE 0.019 0.001 PHE D 341 TRP 0.046 0.001 TRP A 327 HIS 0.022 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00352 (22697) covalent geometry : angle 0.57844 (30734) SS BOND : bond 0.00545 ( 3) SS BOND : angle 1.46282 ( 6) hydrogen bonds : bond 0.04448 ( 1502) hydrogen bonds : angle 3.91553 ( 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 394 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8494 (tpp) cc_final: 0.8255 (mmm) REVERT: A 81 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 394 HIS cc_start: 0.7799 (m-70) cc_final: 0.7538 (m-70) REVERT: A 400 PRO cc_start: 0.8513 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8422 (mp) REVERT: A 423 TRP cc_start: 0.8288 (t-100) cc_final: 0.7480 (t60) REVERT: A 492 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: A 629 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: A 661 PHE cc_start: 0.8003 (t80) cc_final: 0.7608 (t80) REVERT: A 709 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8158 (tt0) REVERT: A 736 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 112 ASP cc_start: 0.8341 (p0) cc_final: 0.8034 (p0) REVERT: B 204 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8864 (ttpp) REVERT: B 260 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: B 425 TYR cc_start: 0.8011 (m-80) cc_final: 0.7638 (m-80) REVERT: B 504 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7094 (t80) REVERT: B 530 MET cc_start: 0.7964 (mtt) cc_final: 0.6779 (tmm) REVERT: B 588 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7196 (tt) REVERT: B 606 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 724 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7973 (tptm) REVERT: B 727 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8184 (mtm-85) REVERT: B 729 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8844 (mm-30) REVERT: B 759 GLU cc_start: 0.8768 (tp30) cc_final: 0.8497 (tp30) REVERT: C 17 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7730 (mmm160) REVERT: C 54 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (mt-10) REVERT: C 118 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7379 (m-80) REVERT: C 286 ASP cc_start: 0.8657 (t0) cc_final: 0.7938 (t0) REVERT: C 335 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8690 (mpp) REVERT: C 410 TRP cc_start: 0.8238 (OUTLIER) cc_final: 0.7543 (m-90) REVERT: C 421 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7753 (pt0) REVERT: C 430 TYR cc_start: 0.8341 (t80) cc_final: 0.7911 (t80) REVERT: C 432 HIS cc_start: 0.8726 (m-70) cc_final: 0.8445 (m-70) REVERT: C 518 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 705 ASP cc_start: 0.7954 (t0) cc_final: 0.7684 (t0) REVERT: C 711 GLN cc_start: 0.8701 (tp40) cc_final: 0.7505 (tp40) REVERT: D 50 GLN cc_start: 0.9002 (tt0) cc_final: 0.8593 (tp-100) REVERT: D 66 MET cc_start: 0.9120 (mmm) cc_final: 0.8528 (mmm) REVERT: D 343 MET cc_start: 0.8457 (tpt) cc_final: 0.8159 (tpt) REVERT: D 359 PHE cc_start: 0.8566 (t80) cc_final: 0.8165 (t80) REVERT: D 380 MET cc_start: 0.8659 (mmm) cc_final: 0.8428 (mtm) REVERT: D 465 PRO cc_start: 0.8640 (Cg_exo) cc_final: 0.8390 (Cg_endo) REVERT: D 541 TYR cc_start: 0.8799 (m-80) cc_final: 0.8270 (m-10) REVERT: D 551 ASN cc_start: 0.9101 (t0) cc_final: 0.8778 (t0) REVERT: D 559 GLU cc_start: 0.8587 (tt0) cc_final: 0.8273 (tp30) REVERT: D 652 ASP cc_start: 0.8636 (t0) cc_final: 0.8319 (t0) REVERT: D 736 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: D 740 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7446 (tm-30) REVERT: D 744 LYS cc_start: 0.9199 (mmtm) cc_final: 0.8821 (mmtm) outliers start: 83 outliers final: 42 residues processed: 368 average time/residue: 0.5554 time to fit residues: 235.6103 Evaluate side-chains 358 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 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 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 617 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 738 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 430 TRP Chi-restraints excluded: chain B residue 445 GLU 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 553 ILE 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 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 410 TRP Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU 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 262 SER Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 444 SER 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 703 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: 1.9990 chunk 183 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 732 GLN B 766 GLN ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 177 ASN ** 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 = 0.3615 r_free = 0.3615 target = 0.111621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.079658 restraints weight = 39591.953| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.70 r_work: 0.2882 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22700 Z= 0.152 Angle : 0.591 17.562 30740 Z= 0.295 Chirality : 0.039 0.390 3478 Planarity : 0.004 0.055 3820 Dihedral : 8.132 167.466 3266 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.51 % Allowed : 18.50 % Favored : 78.00 % 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: 2.74 (0.16), residues: 2673 helix: 2.36 (0.11), residues: 1986 sheet: None (None), residues: 0 loop : 0.21 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 324 TYR 0.020 0.001 TYR C 524 PHE 0.020 0.001 PHE D 341 TRP 0.042 0.001 TRP C 322 HIS 0.022 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00354 (22697) covalent geometry : angle 0.59063 (30734) SS BOND : bond 0.00099 ( 3) SS BOND : angle 1.35435 ( 6) hydrogen bonds : bond 0.04409 ( 1502) hydrogen bonds : angle 3.90595 ( 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 398 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 314 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8514 (tpp) cc_final: 0.8228 (mmm) REVERT: A 81 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8425 (mt-10) REVERT: A 394 HIS cc_start: 0.7807 (m-70) cc_final: 0.7532 (m-70) REVERT: A 400 PRO cc_start: 0.8508 (Cg_exo) cc_final: 0.8182 (Cg_endo) REVERT: A 419 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8350 (mp) REVERT: A 423 TRP cc_start: 0.8261 (t-100) cc_final: 0.7407 (t60) REVERT: A 492 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8043 (mtp180) REVERT: A 629 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: A 652 ASP cc_start: 0.8504 (t0) cc_final: 0.7482 (p0) REVERT: A 661 PHE cc_start: 0.7996 (t80) cc_final: 0.7636 (t80) REVERT: A 709 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8171 (tt0) REVERT: A 733 LYS cc_start: 0.8616 (mttm) cc_final: 0.8379 (mtmt) REVERT: A 736 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7768 (mt-10) REVERT: B 112 ASP cc_start: 0.8353 (p0) cc_final: 0.8061 (p0) REVERT: B 204 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8888 (ttpp) REVERT: B 260 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: B 425 TYR cc_start: 0.7987 (m-80) cc_final: 0.7612 (m-80) REVERT: B 504 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 530 MET cc_start: 0.7928 (mtt) cc_final: 0.6781 (ttp) REVERT: B 535 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8031 (mm-40) REVERT: B 588 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 724 LYS cc_start: 0.8415 (ttpt) cc_final: 0.7997 (tptm) REVERT: B 727 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8136 (mtm-85) REVERT: B 729 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8839 (mm-30) REVERT: B 759 GLU cc_start: 0.8785 (tp30) cc_final: 0.8542 (tp30) REVERT: C 17 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7748 (mmm160) REVERT: C 54 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: C 79 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: C 118 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: C 240 GLU cc_start: 0.8864 (mp0) cc_final: 0.8602 (mp0) REVERT: C 286 ASP cc_start: 0.8595 (t0) cc_final: 0.7828 (t0) REVERT: C 335 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8649 (mpp) REVERT: C 410 TRP cc_start: 0.8226 (OUTLIER) cc_final: 0.7457 (m-90) REVERT: C 421 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: C 430 TYR cc_start: 0.8243 (t80) cc_final: 0.7766 (t80) REVERT: C 432 HIS cc_start: 0.8692 (m-70) cc_final: 0.8398 (m-70) REVERT: C 518 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8389 (tt) REVERT: C 705 ASP cc_start: 0.7960 (t0) cc_final: 0.7693 (t0) REVERT: C 711 GLN cc_start: 0.8431 (tp40) cc_final: 0.8027 (tp40) REVERT: D 50 GLN cc_start: 0.8990 (tt0) cc_final: 0.8590 (tp-100) REVERT: D 66 MET cc_start: 0.9116 (mmm) cc_final: 0.8508 (mmm) REVERT: D 331 LEU cc_start: 0.9085 (tt) cc_final: 0.8673 (tp) REVERT: D 335 MET cc_start: 0.9347 (mmm) cc_final: 0.8961 (mpp) REVERT: D 343 MET cc_start: 0.8445 (tpt) cc_final: 0.8140 (tpt) REVERT: D 358 LEU cc_start: 0.8889 (mt) cc_final: 0.8575 (mm) REVERT: D 359 PHE cc_start: 0.8552 (t80) cc_final: 0.8117 (t80) REVERT: D 380 MET cc_start: 0.8616 (mmm) cc_final: 0.8374 (mtm) REVERT: D 422 MET cc_start: 0.8712 (mtt) cc_final: 0.8482 (mmt) REVERT: D 465 PRO cc_start: 0.8825 (Cg_exo) cc_final: 0.8518 (Cg_endo) REVERT: D 541 TYR cc_start: 0.8794 (m-80) cc_final: 0.8277 (m-10) REVERT: D 551 ASN cc_start: 0.9101 (t0) cc_final: 0.8807 (t0) REVERT: D 559 GLU cc_start: 0.8536 (tt0) cc_final: 0.8302 (tp30) REVERT: D 652 ASP cc_start: 0.8627 (t0) cc_final: 0.8296 (t0) REVERT: D 740 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7462 (tm-30) REVERT: D 744 LYS cc_start: 0.9161 (mmtm) cc_final: 0.8849 (mmtm) outliers start: 84 outliers final: 43 residues processed: 368 average time/residue: 0.6068 time to fit residues: 256.7520 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 : 0.828 ------------------------------------------------------------------------------- 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 108 VAL Chi-restraints excluded: chain A residue 182 VAL 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 471 MET Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 617 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 738 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 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU 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 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 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 410 TRP Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 526 LEU 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 262 SER 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 455 VAL Chi-restraints excluded: chain D residue 513 MET 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 703 HIS 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: 3.9990 chunk 112 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 43 optimal weight: 0.0870 chunk 165 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.114506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.083183 restraints weight = 39460.346| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.72 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22700 Z= 0.121 Angle : 0.594 16.946 30740 Z= 0.294 Chirality : 0.038 0.420 3478 Planarity : 0.004 0.054 3820 Dihedral : 7.934 164.414 3264 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.63 % Allowed : 19.50 % Favored : 77.87 % 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: 2.84 (0.16), residues: 2673 helix: 2.44 (0.11), residues: 1983 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 324 TYR 0.020 0.001 TYR C 446 PHE 0.019 0.001 PHE D 341 TRP 0.043 0.001 TRP C 322 HIS 0.015 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00264 (22697) covalent geometry : angle 0.59370 (30734) SS BOND : bond 0.00092 ( 3) SS BOND : angle 1.03714 ( 6) hydrogen bonds : bond 0.04071 ( 1502) hydrogen bonds : angle 3.84755 ( 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 383 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 320 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8521 (tpp) cc_final: 0.8196 (mmm) REVERT: A 394 HIS cc_start: 0.7818 (m-70) cc_final: 0.7532 (m-70) REVERT: A 400 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8114 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8251 (t-100) cc_final: 0.7415 (t60) REVERT: A 492 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8047 (mtp180) REVERT: A 629 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7376 (mp-120) REVERT: A 652 ASP cc_start: 0.8389 (t0) cc_final: 0.7393 (p0) REVERT: A 661 PHE cc_start: 0.7984 (t80) cc_final: 0.7728 (t80) REVERT: A 709 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8213 (tt0) REVERT: A 733 LYS cc_start: 0.8631 (mttm) cc_final: 0.8385 (mtmt) REVERT: A 736 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7882 (mt-10) REVERT: B 112 ASP cc_start: 0.8342 (p0) cc_final: 0.8047 (p0) REVERT: B 204 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.8908 (ttpp) REVERT: B 260 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: B 425 TYR cc_start: 0.8049 (m-80) cc_final: 0.7711 (m-80) REVERT: B 504 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.7134 (t80) REVERT: B 530 MET cc_start: 0.7724 (mtt) cc_final: 0.6872 (ttp) REVERT: B 535 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7844 (mm-40) REVERT: B 549 PHE cc_start: 0.7678 (m-10) cc_final: 0.7062 (t80) REVERT: B 588 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7185 (tt) REVERT: B 724 LYS cc_start: 0.8433 (ttpt) cc_final: 0.8010 (tptm) REVERT: B 727 ARG cc_start: 0.8361 (mtp85) cc_final: 0.8032 (mtm-85) REVERT: B 729 GLU cc_start: 0.9019 (OUTLIER) cc_final: 0.8814 (mm-30) REVERT: B 759 GLU cc_start: 0.8804 (tp30) cc_final: 0.8510 (tp30) REVERT: C 17 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7704 (mmm160) REVERT: C 54 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: C 118 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: C 240 GLU cc_start: 0.8868 (mp0) cc_final: 0.8620 (mp0) REVERT: C 286 ASP cc_start: 0.8647 (t0) cc_final: 0.7904 (t0) REVERT: C 335 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8667 (mpp) REVERT: C 358 LEU cc_start: 0.9215 (mp) cc_final: 0.8937 (pp) REVERT: C 410 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7461 (m-90) REVERT: C 421 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: C 432 HIS cc_start: 0.8737 (m-70) cc_final: 0.8435 (m-70) REVERT: C 705 ASP cc_start: 0.7864 (t0) cc_final: 0.7641 (t0) REVERT: C 711 GLN cc_start: 0.8378 (tp40) cc_final: 0.7950 (tp40) REVERT: D 50 GLN cc_start: 0.8985 (tt0) cc_final: 0.8588 (tp-100) REVERT: D 66 MET cc_start: 0.9148 (mmm) cc_final: 0.8536 (mmm) REVERT: D 343 MET cc_start: 0.8412 (tpt) cc_final: 0.8113 (tpt) REVERT: D 358 LEU cc_start: 0.8891 (mt) cc_final: 0.8548 (mm) REVERT: D 359 PHE cc_start: 0.8501 (t80) cc_final: 0.8063 (t80) REVERT: D 422 MET cc_start: 0.8712 (mtt) cc_final: 0.8462 (mmt) REVERT: D 432 HIS cc_start: 0.8608 (p90) cc_final: 0.8354 (m-70) REVERT: D 465 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8404 (Cg_endo) REVERT: D 541 TYR cc_start: 0.8811 (m-80) cc_final: 0.8288 (m-10) REVERT: D 551 ASN cc_start: 0.9101 (t0) cc_final: 0.8813 (t0) REVERT: D 559 GLU cc_start: 0.8547 (tt0) cc_final: 0.8321 (tp30) REVERT: D 652 ASP cc_start: 0.8617 (t0) cc_final: 0.8287 (t0) REVERT: D 736 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: D 740 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 744 LYS cc_start: 0.9159 (mmtm) cc_final: 0.8898 (mmtm) outliers start: 63 outliers final: 32 residues processed: 361 average time/residue: 0.5619 time to fit residues: 233.0628 Evaluate side-chains 352 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 305 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 471 MET Chi-restraints excluded: chain A residue 492 ARG 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 738 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 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU 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 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 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 410 TRP Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain D residue 116 LEU 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 395 VAL Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 517 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 0.0970 chunk 11 optimal weight: 0.3980 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** 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 = 0.3682 r_free = 0.3682 target = 0.113801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082397 restraints weight = 39652.153| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.73 r_work: 0.2969 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22700 Z= 0.138 Angle : 0.632 16.416 30740 Z= 0.313 Chirality : 0.039 0.472 3478 Planarity : 0.004 0.066 3820 Dihedral : 7.884 161.354 3264 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.25 % Allowed : 20.38 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.43 (0.11), residues: 1983 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 324 TYR 0.023 0.001 TYR C 446 PHE 0.020 0.001 PHE D 341 TRP 0.045 0.001 TRP C 322 HIS 0.014 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00318 (22697) covalent geometry : angle 0.63211 (30734) SS BOND : bond 0.00094 ( 3) SS BOND : angle 1.04323 ( 6) hydrogen bonds : bond 0.04205 ( 1502) hydrogen bonds : angle 3.86138 ( 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 371 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 317 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8529 (tpp) cc_final: 0.8198 (mmm) REVERT: A 81 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8327 (mt-10) REVERT: A 136 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6634 (t80) REVERT: A 286 ASP cc_start: 0.8328 (m-30) cc_final: 0.7983 (p0) REVERT: A 394 HIS cc_start: 0.7855 (m-70) cc_final: 0.7605 (m-70) REVERT: A 400 PRO cc_start: 0.8456 (Cg_exo) cc_final: 0.8116 (Cg_endo) REVERT: A 423 TRP cc_start: 0.8247 (t-100) cc_final: 0.7438 (t60) REVERT: A 492 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8053 (mtp180) REVERT: A 629 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7337 (mp-120) REVERT: A 652 ASP cc_start: 0.8367 (t0) cc_final: 0.7365 (p0) REVERT: A 661 PHE cc_start: 0.7965 (t80) cc_final: 0.7705 (t80) REVERT: A 709 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8190 (tt0) REVERT: A 733 LYS cc_start: 0.8619 (mttm) cc_final: 0.8388 (mtmt) REVERT: A 736 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7856 (mt-10) REVERT: B 112 ASP cc_start: 0.8342 (p0) cc_final: 0.8051 (p0) REVERT: B 204 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9184 (tttp) REVERT: B 260 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: B 305 MET cc_start: 0.6864 (mmp) cc_final: 0.6255 (mmp) REVERT: B 425 TYR cc_start: 0.8047 (m-80) cc_final: 0.7697 (m-80) REVERT: B 504 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7124 (t80) REVERT: B 530 MET cc_start: 0.7797 (mtt) cc_final: 0.7005 (ttp) REVERT: B 535 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7963 (mm-40) REVERT: B 549 PHE cc_start: 0.7642 (m-10) cc_final: 0.7038 (t80) REVERT: B 588 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7167 (tt) REVERT: B 724 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8053 (tptm) REVERT: B 727 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8052 (mtm-85) REVERT: B 759 GLU cc_start: 0.8819 (tp30) cc_final: 0.8559 (tp30) REVERT: C 17 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7719 (mmm160) REVERT: C 54 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8289 (mt-10) REVERT: C 240 GLU cc_start: 0.8885 (mp0) cc_final: 0.8640 (mp0) REVERT: C 286 ASP cc_start: 0.8639 (t0) cc_final: 0.7893 (t0) REVERT: C 335 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8657 (mpp) REVERT: C 358 LEU cc_start: 0.9239 (mp) cc_final: 0.8973 (pp) REVERT: C 410 TRP cc_start: 0.8276 (OUTLIER) cc_final: 0.7460 (m-90) REVERT: C 421 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7811 (pt0) REVERT: C 432 HIS cc_start: 0.8739 (m-70) cc_final: 0.8462 (m-70) REVERT: C 705 ASP cc_start: 0.7848 (t0) cc_final: 0.7619 (t0) REVERT: C 711 GLN cc_start: 0.8363 (tp40) cc_final: 0.7919 (tp40) REVERT: D 50 GLN cc_start: 0.9003 (tt0) cc_final: 0.8599 (tp-100) REVERT: D 66 MET cc_start: 0.9128 (mmm) cc_final: 0.8571 (mmm) REVERT: D 324 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7660 (ttm110) REVERT: D 343 MET cc_start: 0.8438 (tpt) cc_final: 0.8105 (tpt) REVERT: D 358 LEU cc_start: 0.8895 (mt) cc_final: 0.8602 (mm) REVERT: D 359 PHE cc_start: 0.8499 (t80) cc_final: 0.8071 (t80) REVERT: D 422 MET cc_start: 0.8725 (mtt) cc_final: 0.8483 (mmt) REVERT: D 465 PRO cc_start: 0.8729 (Cg_exo) cc_final: 0.8440 (Cg_endo) REVERT: D 541 TYR cc_start: 0.8817 (m-80) cc_final: 0.8283 (m-10) REVERT: D 551 ASN cc_start: 0.9142 (t0) cc_final: 0.8864 (t0) REVERT: D 559 GLU cc_start: 0.8570 (tt0) cc_final: 0.8325 (tp30) REVERT: D 629 GLN cc_start: 0.8718 (mt0) cc_final: 0.8492 (mt0) REVERT: D 652 ASP cc_start: 0.8635 (t0) cc_final: 0.8307 (t0) REVERT: D 736 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8615 (mt-10) REVERT: D 740 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7420 (tm-30) REVERT: D 744 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8877 (mmtm) outliers start: 54 outliers final: 33 residues processed: 351 average time/residue: 0.5457 time to fit residues: 220.5838 Evaluate side-chains 347 residues out of total 2422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 300 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 136 PHE Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 250 LEU 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 629 GLN 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 430 TRP Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 445 GLU 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 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 410 TRP Chi-restraints excluded: chain C residue 421 GLU Chi-restraints excluded: chain C residue 434 TRP Chi-restraints excluded: chain C residue 526 LEU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 619 MET 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 211 LEU Chi-restraints excluded: chain D residue 250 LEU 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 98 optimal weight: 0.4980 chunk 119 optimal weight: 0.0470 chunk 165 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 254 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 250 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 244 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 386 GLN ** D 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.114763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.083401 restraints weight = 39606.608| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.73 r_work: 0.2987 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22700 Z= 0.124 Angle : 0.619 16.332 30740 Z= 0.307 Chirality : 0.039 0.359 3478 Planarity : 0.004 0.053 3820 Dihedral : 7.766 158.356 3264 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 2.17 % Allowed : 20.84 % Favored : 76.99 % 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: 2.49 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 324 TYR 0.025 0.001 TYR C 446 PHE 0.019 0.001 PHE A 339 TRP 0.047 0.001 TRP C 322 HIS 0.015 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00276 (22697) covalent geometry : angle 0.61846 (30734) SS BOND : bond 0.00095 ( 3) SS BOND : angle 0.98184 ( 6) hydrogen bonds : bond 0.04032 ( 1502) hydrogen bonds : angle 3.84831 ( 4374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7528.19 seconds wall clock time: 129 minutes 4.58 seconds (7744.58 seconds total)