Starting phenix.real_space_refine on Tue Jul 29 01:44:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.map" model { file = "/net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vjm_21219/07_2025/6vjm_21219.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6837 2.51 5 N 1759 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5267 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 5212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5212 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 20.81, per 1000 atoms: 1.96 Number of scatterers: 10629 At special positions: 0 Unit cell: (83.16, 106.92, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1979 8.00 N 1759 7.00 C 6837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.04 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1006 " - " ASN A 409 " " NAG B1002 " - " ASN B 453 " " NAG C 1 " - " ASN A 440 " " NAG D 1 " - " ASN A 482 " " NAG E 1 " - " ASN A 514 " " NAG F 1 " - " ASN B 404 " Time building additional restraints: 6.05 Conformation dependent library (CDL) restraints added in 4.3 seconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 54.0% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.701A pdb=" N GLN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.756A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.521A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.662A pdb=" N SER A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.707A pdb=" N LEU A 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.043A pdb=" N TRP A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 4.272A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.627A pdb=" N VAL A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.156A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 467 through 485 removed outlier: 4.107A pdb=" N TYR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.657A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.634A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 644 Processing helix chain 'A' and resid 658 through 693 removed outlier: 4.385A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 685 " --> pdb=" O MET A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 732 removed outlier: 4.264A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 732 " --> pdb=" O TRP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 removed outlier: 3.616A pdb=" N TYR A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 825 removed outlier: 3.781A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 832 through 853 Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.901A pdb=" N MET A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 861 " --> pdb=" O MET A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 91 removed outlier: 3.891A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Proline residue: B 79 - end of helix Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 135 through 146 removed outlier: 4.105A pdb=" N ILE B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.129A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.836A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.701A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.004A pdb=" N SER B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.791A pdb=" N ALA B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.869A pdb=" N GLU B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 292 " --> pdb=" O TRP B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 288 through 292' Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.159A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 4.227A pdb=" N ARG B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 378 removed outlier: 3.913A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.931A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 509 removed outlier: 4.195A pdb=" N ILE B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.508A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.743A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 550 " --> pdb=" O LYS B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 551 through 583 removed outlier: 3.867A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 619 removed outlier: 3.641A pdb=" N MET B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 619 " --> pdb=" O TRP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 678 removed outlier: 4.023A pdb=" N PHE B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 672 " --> pdb=" O MET B 668 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 676 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 712 removed outlier: 4.573A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 741 removed outlier: 4.384A pdb=" N THR B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 175 removed outlier: 3.689A pdb=" N HIS A 216 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.082A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 343 removed outlier: 7.374A pdb=" N ILE A 309 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLN A 341 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 311 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 362 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ILE A 393 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY A 364 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.501A pdb=" N PHE A 518 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 583 removed outlier: 3.701A pdb=" N SER A 753 " --> pdb=" O THR A 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 8.625A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 153 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.581A pdb=" N SER B 227 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR B 200 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR B 229 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 202 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR B 314 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 431 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.691A pdb=" N PHE B 408 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.616A pdb=" N THR B 448 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 474 removed outlier: 6.451A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 646 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1569 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: 9.04 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3356 1.35 - 1.47: 2723 1.47 - 1.59: 4711 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 10874 Sorted by residual: bond pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.17e-02 7.31e+03 9.69e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CA VAL A 349 " pdb=" CB VAL A 349 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14399 2.44 - 4.88: 315 4.88 - 7.32: 50 7.32 - 9.76: 21 9.76 - 12.20: 5 Bond angle restraints: 14790 Sorted by residual: angle pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 121.19 130.65 -9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" C GLN A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C GLN A 658 " pdb=" N PHE A 659 " pdb=" CA PHE A 659 " ideal model delta sigma weight residual 120.09 126.20 -6.11 1.25e+00 6.40e-01 2.39e+01 angle pdb=" C ASN B 650 " pdb=" N THR B 651 " pdb=" CA THR B 651 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C PHE A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 121.91 116.28 5.63 1.35e+00 5.49e-01 1.74e+01 ... (remaining 14785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5868 17.39 - 34.77: 581 34.77 - 52.16: 108 52.16 - 69.55: 22 69.55 - 86.93: 4 Dihedral angle restraints: 6583 sinusoidal: 2601 harmonic: 3982 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual -86.00 -24.79 -61.21 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual -86.00 -33.83 -52.17 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA THR A 704 " pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1403 0.073 - 0.146: 277 0.146 - 0.219: 29 0.219 - 0.292: 2 0.292 - 0.366: 2 Chirality restraints: 1713 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 409 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE A 645 " pdb=" N PHE A 645 " pdb=" C PHE A 645 " pdb=" CB PHE A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1710 not shown) Planarity restraints: 1866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 320 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 321 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 467 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 468 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 95 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 96 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.026 5.00e-02 4.00e+02 ... (remaining 1863 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3336 2.82 - 3.34: 9929 3.34 - 3.86: 17923 3.86 - 4.38: 19020 4.38 - 4.90: 31950 Nonbonded interactions: 82158 Sorted by model distance: nonbonded pdb=" OD1 ASP A 721 " pdb=" OH TYR A 776 " model vdw 2.297 3.040 nonbonded pdb=" O ILE B 452 " pdb=" OG1 THR B 455 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 379 " pdb=" OE1 GLU A 414 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLN A 444 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 247 " pdb=" OG SER A 250 " model vdw 2.314 3.040 ... (remaining 82153 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 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 300.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 67.540 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:6.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 376.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10892 Z= 0.239 Angle : 0.974 18.863 14837 Z= 0.497 Chirality : 0.058 0.366 1713 Planarity : 0.006 0.069 1860 Dihedral : 14.174 86.933 3996 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.18), residues: 1357 helix: -2.44 (0.14), residues: 674 sheet: -2.27 (0.35), residues: 182 loop : -3.64 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 558 HIS 0.006 0.001 HIS A 802 PHE 0.022 0.002 PHE A 645 TYR 0.019 0.002 TYR B 663 ARG 0.004 0.000 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.01201 ( 6) link_NAG-ASN : angle 6.23252 ( 18) link_BETA1-4 : bond 0.00784 ( 4) link_BETA1-4 : angle 6.59087 ( 12) hydrogen bonds : bond 0.10465 ( 531) hydrogen bonds : angle 6.19622 ( 1569) link_BETA1-6 : bond 0.00180 ( 1) link_BETA1-6 : angle 3.36015 ( 3) SS BOND : bond 0.00253 ( 7) SS BOND : angle 1.82670 ( 14) covalent geometry : bond 0.00485 (10874) covalent geometry : angle 0.92971 (14790) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8978 (tt) cc_final: 0.8524 (mp) REVERT: A 178 MET cc_start: 0.8771 (mmt) cc_final: 0.8267 (mmm) REVERT: A 582 LYS cc_start: 0.8865 (tttt) cc_final: 0.8544 (tmtt) REVERT: A 807 MET cc_start: 0.8096 (tpt) cc_final: 0.7843 (tpt) REVERT: B 435 ARG cc_start: 0.9344 (ptp90) cc_final: 0.9143 (mtm-85) REVERT: B 604 MET cc_start: 0.7595 (ptt) cc_final: 0.7312 (ptp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.4435 time to fit residues: 82.7922 Evaluate side-chains 90 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 293 HIS A 353 ASN A 508 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 HIS B 87 GLN B 126 ASN B 192 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 401 ASN B 414 GLN ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 503 ASN B 506 ASN B 698 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.071036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.060249 restraints weight = 60492.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.061691 restraints weight = 36481.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.062673 restraints weight = 25273.462| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10892 Z= 0.128 Angle : 0.691 13.075 14837 Z= 0.336 Chirality : 0.045 0.369 1713 Planarity : 0.005 0.057 1860 Dihedral : 6.075 47.239 1692 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.52 % Allowed : 13.23 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.21), residues: 1357 helix: -0.71 (0.19), residues: 677 sheet: -2.05 (0.35), residues: 199 loop : -3.21 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.003 0.001 HIS A 802 PHE 0.021 0.001 PHE A 645 TYR 0.019 0.001 TYR B 169 ARG 0.005 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 6) link_NAG-ASN : angle 4.94932 ( 18) link_BETA1-4 : bond 0.00722 ( 4) link_BETA1-4 : angle 4.57525 ( 12) hydrogen bonds : bond 0.03953 ( 531) hydrogen bonds : angle 4.95630 ( 1569) link_BETA1-6 : bond 0.00227 ( 1) link_BETA1-6 : angle 2.40413 ( 3) SS BOND : bond 0.00198 ( 7) SS BOND : angle 1.15123 ( 14) covalent geometry : bond 0.00271 (10874) covalent geometry : angle 0.65520 (14790) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9034 (tt) cc_final: 0.8684 (mt) REVERT: A 178 MET cc_start: 0.8785 (mmt) cc_final: 0.8230 (mmm) REVERT: A 582 LYS cc_start: 0.8879 (tttt) cc_final: 0.8556 (tmtt) REVERT: A 846 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: B 259 MET cc_start: 0.8237 (tpp) cc_final: 0.7973 (mtt) REVERT: B 320 GLU cc_start: 0.8135 (tp30) cc_final: 0.7920 (tp30) REVERT: B 628 TYR cc_start: 0.9044 (t80) cc_final: 0.8583 (t80) outliers start: 27 outliers final: 14 residues processed: 127 average time/residue: 0.2104 time to fit residues: 40.3668 Evaluate side-chains 112 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN B 126 ASN B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.070606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.059935 restraints weight = 62784.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061343 restraints weight = 37940.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062307 restraints weight = 26328.170| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10892 Z= 0.136 Angle : 0.672 12.674 14837 Z= 0.328 Chirality : 0.045 0.355 1713 Planarity : 0.004 0.051 1860 Dihedral : 5.863 48.438 1692 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.26 % Allowed : 14.73 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.22), residues: 1357 helix: 0.03 (0.20), residues: 674 sheet: -2.03 (0.34), residues: 208 loop : -2.95 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.021 0.001 PHE A 645 TYR 0.018 0.001 TYR B 169 ARG 0.003 0.000 ARG B 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00863 ( 6) link_NAG-ASN : angle 4.85081 ( 18) link_BETA1-4 : bond 0.00480 ( 4) link_BETA1-4 : angle 4.13605 ( 12) hydrogen bonds : bond 0.03825 ( 531) hydrogen bonds : angle 4.73535 ( 1569) link_BETA1-6 : bond 0.00146 ( 1) link_BETA1-6 : angle 2.19063 ( 3) SS BOND : bond 0.00162 ( 7) SS BOND : angle 1.08633 ( 14) covalent geometry : bond 0.00291 (10874) covalent geometry : angle 0.63905 (14790) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.9049 (tt) cc_final: 0.8689 (mt) REVERT: A 178 MET cc_start: 0.8776 (mmt) cc_final: 0.8209 (mmm) REVERT: A 328 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8470 (tm-30) REVERT: A 415 MET cc_start: 0.7666 (mmt) cc_final: 0.7319 (mmm) REVERT: A 582 LYS cc_start: 0.8882 (tttt) cc_final: 0.8549 (tmtt) REVERT: A 810 TYR cc_start: 0.7870 (m-80) cc_final: 0.7635 (m-80) REVERT: A 846 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6990 (m-80) REVERT: B 403 MET cc_start: 0.9088 (tpt) cc_final: 0.8861 (tpp) REVERT: B 628 TYR cc_start: 0.9081 (t80) cc_final: 0.8722 (t80) outliers start: 35 outliers final: 22 residues processed: 122 average time/residue: 0.2282 time to fit residues: 44.1582 Evaluate side-chains 113 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 422 HIS A 457 HIS A 658 GLN B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 ASN B 698 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.067122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.056710 restraints weight = 63785.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058049 restraints weight = 38253.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058924 restraints weight = 26571.259| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 10892 Z= 0.316 Angle : 0.827 12.115 14837 Z= 0.418 Chirality : 0.049 0.358 1713 Planarity : 0.005 0.071 1860 Dihedral : 6.548 48.599 1692 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.63 % Allowed : 17.80 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.23), residues: 1357 helix: -0.04 (0.20), residues: 663 sheet: -2.14 (0.35), residues: 200 loop : -2.84 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 558 HIS 0.005 0.001 HIS A 689 PHE 0.030 0.003 PHE B 501 TYR 0.022 0.002 TYR B 663 ARG 0.004 0.001 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00949 ( 6) link_NAG-ASN : angle 4.93921 ( 18) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 4.20515 ( 12) hydrogen bonds : bond 0.04780 ( 531) hydrogen bonds : angle 5.23236 ( 1569) link_BETA1-6 : bond 0.00110 ( 1) link_BETA1-6 : angle 2.87102 ( 3) SS BOND : bond 0.00379 ( 7) SS BOND : angle 2.13933 ( 14) covalent geometry : bond 0.00669 (10874) covalent geometry : angle 0.79785 (14790) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8855 (mmt) cc_final: 0.8277 (mmm) REVERT: A 582 LYS cc_start: 0.8900 (tttt) cc_final: 0.8557 (tmtt) REVERT: A 846 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: B 272 MET cc_start: 0.9108 (mmm) cc_final: 0.8392 (tpp) REVERT: B 320 GLU cc_start: 0.8537 (tp30) cc_final: 0.8299 (tp30) REVERT: B 403 MET cc_start: 0.9041 (tpt) cc_final: 0.8834 (tpp) outliers start: 39 outliers final: 28 residues processed: 123 average time/residue: 0.1733 time to fit residues: 33.5028 Evaluate side-chains 115 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.8980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.067961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.057541 restraints weight = 62934.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.058872 restraints weight = 37538.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059829 restraints weight = 26055.204| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10892 Z= 0.214 Angle : 0.750 12.088 14837 Z= 0.371 Chirality : 0.047 0.350 1713 Planarity : 0.004 0.056 1860 Dihedral : 6.354 49.194 1692 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 3.73 % Allowed : 19.29 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1357 helix: 0.05 (0.20), residues: 672 sheet: -2.12 (0.34), residues: 204 loop : -2.77 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.026 0.002 PHE A 645 TYR 0.019 0.002 TYR B 663 ARG 0.002 0.000 ARG B 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 6) link_NAG-ASN : angle 4.81908 ( 18) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 3.92746 ( 12) hydrogen bonds : bond 0.04389 ( 531) hydrogen bonds : angle 5.05036 ( 1569) link_BETA1-6 : bond 0.00121 ( 1) link_BETA1-6 : angle 2.60684 ( 3) SS BOND : bond 0.00321 ( 7) SS BOND : angle 2.18504 ( 14) covalent geometry : bond 0.00460 (10874) covalent geometry : angle 0.71972 (14790) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8821 (mmt) cc_final: 0.8330 (mmm) REVERT: A 415 MET cc_start: 0.7290 (mmt) cc_final: 0.6956 (mmt) REVERT: A 582 LYS cc_start: 0.8893 (tttt) cc_final: 0.8542 (tmtt) REVERT: A 846 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6933 (m-80) REVERT: B 272 MET cc_start: 0.9128 (mmm) cc_final: 0.8509 (tpp) REVERT: B 403 MET cc_start: 0.9021 (tpt) cc_final: 0.8783 (tpp) REVERT: B 630 MET cc_start: 0.8960 (pmm) cc_final: 0.8758 (pmm) REVERT: B 702 MET cc_start: 0.8961 (mmm) cc_final: 0.8639 (mmt) outliers start: 40 outliers final: 30 residues processed: 126 average time/residue: 0.1795 time to fit residues: 35.4872 Evaluate side-chains 120 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.068950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058589 restraints weight = 62621.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059954 restraints weight = 37657.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.060848 restraints weight = 26112.732| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10892 Z= 0.145 Angle : 0.712 12.309 14837 Z= 0.344 Chirality : 0.047 0.350 1713 Planarity : 0.004 0.049 1860 Dihedral : 6.119 49.484 1692 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.10 % Allowed : 19.20 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.23), residues: 1357 helix: 0.22 (0.20), residues: 675 sheet: -2.07 (0.34), residues: 203 loop : -2.75 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.023 0.001 PHE A 645 TYR 0.016 0.001 TYR B 663 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00857 ( 6) link_NAG-ASN : angle 4.79103 ( 18) link_BETA1-4 : bond 0.00395 ( 4) link_BETA1-4 : angle 3.68202 ( 12) hydrogen bonds : bond 0.04086 ( 531) hydrogen bonds : angle 4.82926 ( 1569) link_BETA1-6 : bond 0.00176 ( 1) link_BETA1-6 : angle 2.24049 ( 3) SS BOND : bond 0.00264 ( 7) SS BOND : angle 1.63788 ( 14) covalent geometry : bond 0.00313 (10874) covalent geometry : angle 0.68285 (14790) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 93 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8940 (tt) cc_final: 0.8477 (mp) REVERT: A 178 MET cc_start: 0.8787 (mmt) cc_final: 0.8203 (mmm) REVERT: A 415 MET cc_start: 0.7263 (mmt) cc_final: 0.6997 (mmt) REVERT: A 441 MET cc_start: 0.8358 (ttm) cc_final: 0.7942 (mmt) REVERT: A 582 LYS cc_start: 0.8912 (tttt) cc_final: 0.8565 (tmtt) REVERT: A 846 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6949 (m-80) REVERT: B 153 GLN cc_start: 0.8501 (tp40) cc_final: 0.8188 (tp40) REVERT: B 272 MET cc_start: 0.9093 (mmm) cc_final: 0.8485 (tpp) REVERT: B 320 GLU cc_start: 0.8340 (tp30) cc_final: 0.8122 (tp30) REVERT: B 647 HIS cc_start: 0.8331 (OUTLIER) cc_final: 0.7836 (m-70) REVERT: B 702 MET cc_start: 0.9051 (mmm) cc_final: 0.8625 (mmt) outliers start: 44 outliers final: 30 residues processed: 131 average time/residue: 0.1753 time to fit residues: 35.8877 Evaluate side-chains 119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 8.9990 chunk 83 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.068332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057984 restraints weight = 63604.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059290 restraints weight = 38283.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.060216 restraints weight = 26731.242| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10892 Z= 0.186 Angle : 0.727 12.234 14837 Z= 0.355 Chirality : 0.047 0.345 1713 Planarity : 0.004 0.049 1860 Dihedral : 6.137 49.505 1692 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.19 % Allowed : 19.94 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.23), residues: 1357 helix: 0.28 (0.20), residues: 670 sheet: -2.06 (0.34), residues: 206 loop : -2.72 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 PHE 0.023 0.002 PHE A 645 TYR 0.017 0.001 TYR B 663 ARG 0.003 0.000 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 6) link_NAG-ASN : angle 4.82061 ( 18) link_BETA1-4 : bond 0.00344 ( 4) link_BETA1-4 : angle 3.59616 ( 12) hydrogen bonds : bond 0.04112 ( 531) hydrogen bonds : angle 4.86065 ( 1569) link_BETA1-6 : bond 0.00095 ( 1) link_BETA1-6 : angle 2.25747 ( 3) SS BOND : bond 0.00369 ( 7) SS BOND : angle 1.55318 ( 14) covalent geometry : bond 0.00406 (10874) covalent geometry : angle 0.69910 (14790) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 91 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8909 (tt) cc_final: 0.8448 (mp) REVERT: A 178 MET cc_start: 0.8803 (mmt) cc_final: 0.8290 (mmm) REVERT: A 415 MET cc_start: 0.7249 (mmt) cc_final: 0.7021 (mmt) REVERT: A 441 MET cc_start: 0.8368 (ttm) cc_final: 0.7953 (mmp) REVERT: A 582 LYS cc_start: 0.8881 (tttt) cc_final: 0.8521 (tmtt) REVERT: A 846 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6939 (m-80) REVERT: B 153 GLN cc_start: 0.8468 (tp40) cc_final: 0.8154 (tp40) REVERT: B 272 MET cc_start: 0.9086 (mmm) cc_final: 0.8497 (tpp) REVERT: B 320 GLU cc_start: 0.8508 (tp30) cc_final: 0.8234 (tp30) REVERT: B 647 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7845 (m-70) REVERT: B 702 MET cc_start: 0.9017 (mmm) cc_final: 0.8593 (mmt) outliers start: 45 outliers final: 38 residues processed: 126 average time/residue: 0.1893 time to fit residues: 37.5551 Evaluate side-chains 129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 655 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 0.0040 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.069610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.059195 restraints weight = 61704.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060563 restraints weight = 37077.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061490 restraints weight = 25730.617| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10892 Z= 0.123 Angle : 0.704 12.416 14837 Z= 0.335 Chirality : 0.047 0.346 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.948 49.577 1692 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.91 % Allowed : 20.04 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1357 helix: 0.39 (0.20), residues: 677 sheet: -1.89 (0.34), residues: 203 loop : -2.67 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 558 HIS 0.010 0.001 HIS B 647 PHE 0.026 0.001 PHE A 339 TYR 0.014 0.001 TYR B 663 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 6) link_NAG-ASN : angle 4.76585 ( 18) link_BETA1-4 : bond 0.00451 ( 4) link_BETA1-4 : angle 3.40572 ( 12) hydrogen bonds : bond 0.03840 ( 531) hydrogen bonds : angle 4.68762 ( 1569) link_BETA1-6 : bond 0.00344 ( 1) link_BETA1-6 : angle 2.01627 ( 3) SS BOND : bond 0.00269 ( 7) SS BOND : angle 1.27405 ( 14) covalent geometry : bond 0.00266 (10874) covalent geometry : angle 0.67613 (14790) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 94 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8896 (tt) cc_final: 0.8434 (mp) REVERT: A 178 MET cc_start: 0.8755 (mmt) cc_final: 0.8255 (mmm) REVERT: A 441 MET cc_start: 0.8294 (ttm) cc_final: 0.7897 (mmp) REVERT: A 582 LYS cc_start: 0.8895 (tttt) cc_final: 0.8540 (tmtt) REVERT: A 846 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.7010 (m-80) REVERT: B 153 GLN cc_start: 0.8403 (tp40) cc_final: 0.8121 (tp40) REVERT: B 272 MET cc_start: 0.9054 (mmm) cc_final: 0.8518 (tpp) REVERT: B 320 GLU cc_start: 0.8421 (tp30) cc_final: 0.8154 (tp30) REVERT: B 373 MET cc_start: 0.8321 (mmm) cc_final: 0.8062 (mmm) REVERT: B 459 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: B 571 MET cc_start: 0.7817 (tpp) cc_final: 0.7456 (tpp) REVERT: B 630 MET cc_start: 0.9023 (pmm) cc_final: 0.8793 (pmm) REVERT: B 702 MET cc_start: 0.9010 (mmm) cc_final: 0.8550 (mmt) outliers start: 42 outliers final: 35 residues processed: 127 average time/residue: 0.2516 time to fit residues: 54.4457 Evaluate side-chains 126 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 0.0770 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 0.0570 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.070711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060242 restraints weight = 61365.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061650 restraints weight = 36984.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.062586 restraints weight = 25568.261| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10892 Z= 0.113 Angle : 0.713 12.551 14837 Z= 0.334 Chirality : 0.047 0.335 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.730 49.639 1692 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.54 % Allowed : 20.60 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1357 helix: 0.57 (0.20), residues: 674 sheet: -1.70 (0.34), residues: 200 loop : -2.71 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 395 HIS 0.005 0.001 HIS A 802 PHE 0.025 0.001 PHE A 339 TYR 0.011 0.001 TYR B 663 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 6) link_NAG-ASN : angle 4.75636 ( 18) link_BETA1-4 : bond 0.00504 ( 4) link_BETA1-4 : angle 3.16802 ( 12) hydrogen bonds : bond 0.03682 ( 531) hydrogen bonds : angle 4.54009 ( 1569) link_BETA1-6 : bond 0.00258 ( 1) link_BETA1-6 : angle 1.78660 ( 3) SS BOND : bond 0.00394 ( 7) SS BOND : angle 1.32831 ( 14) covalent geometry : bond 0.00240 (10874) covalent geometry : angle 0.68733 (14790) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 96 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8920 (tt) cc_final: 0.8499 (mp) REVERT: A 178 MET cc_start: 0.8712 (mmt) cc_final: 0.8250 (mmm) REVERT: A 194 MET cc_start: 0.9049 (mmm) cc_final: 0.8734 (mmm) REVERT: A 582 LYS cc_start: 0.8892 (tttt) cc_final: 0.8544 (tmtt) REVERT: A 846 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: B 153 GLN cc_start: 0.8424 (tp40) cc_final: 0.8148 (tp40) REVERT: B 320 GLU cc_start: 0.8390 (tp30) cc_final: 0.8115 (tp30) REVERT: B 373 MET cc_start: 0.8432 (mmm) cc_final: 0.8166 (mmm) REVERT: B 459 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: B 571 MET cc_start: 0.7888 (tpp) cc_final: 0.7563 (tpp) REVERT: B 630 MET cc_start: 0.9061 (pmm) cc_final: 0.8848 (pmm) REVERT: B 702 MET cc_start: 0.8911 (mmm) cc_final: 0.8459 (mmt) outliers start: 38 outliers final: 28 residues processed: 125 average time/residue: 0.1836 time to fit residues: 35.9654 Evaluate side-chains 122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 62 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 122 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.065410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055440 restraints weight = 67193.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056713 restraints weight = 39689.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.057593 restraints weight = 27318.810| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.104 10892 Z= 0.512 Angle : 1.049 13.567 14837 Z= 0.537 Chirality : 0.056 0.387 1713 Planarity : 0.006 0.051 1860 Dihedral : 7.185 51.954 1692 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 3.63 % Allowed : 20.50 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.22), residues: 1357 helix: -0.39 (0.19), residues: 670 sheet: -2.10 (0.34), residues: 204 loop : -2.97 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 558 HIS 0.009 0.002 HIS B 192 PHE 0.035 0.004 PHE B 501 TYR 0.034 0.003 TYR A 678 ARG 0.010 0.001 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.01298 ( 6) link_NAG-ASN : angle 5.20999 ( 18) link_BETA1-4 : bond 0.00397 ( 4) link_BETA1-4 : angle 3.81584 ( 12) hydrogen bonds : bond 0.05767 ( 531) hydrogen bonds : angle 5.81913 ( 1569) link_BETA1-6 : bond 0.00321 ( 1) link_BETA1-6 : angle 2.92335 ( 3) SS BOND : bond 0.00575 ( 7) SS BOND : angle 2.29496 ( 14) covalent geometry : bond 0.01071 (10874) covalent geometry : angle 1.02632 (14790) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8920 (mmt) cc_final: 0.8351 (mmm) REVERT: A 582 LYS cc_start: 0.8870 (tttt) cc_final: 0.8498 (tmtt) REVERT: A 846 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: B 153 GLN cc_start: 0.8567 (tp40) cc_final: 0.8254 (tp40) REVERT: B 373 MET cc_start: 0.8526 (mmm) cc_final: 0.8283 (mmm) REVERT: B 403 MET cc_start: 0.9035 (tpt) cc_final: 0.8771 (tpt) REVERT: B 571 MET cc_start: 0.8038 (tpp) cc_final: 0.7660 (tpp) REVERT: B 702 MET cc_start: 0.9110 (mmm) cc_final: 0.8713 (mmt) outliers start: 39 outliers final: 34 residues processed: 121 average time/residue: 0.1767 time to fit residues: 33.7144 Evaluate side-chains 119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 829 GLN Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 42 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.069500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059473 restraints weight = 61951.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.060767 restraints weight = 37342.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061669 restraints weight = 26045.704| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10892 Z= 0.137 Angle : 0.770 13.309 14837 Z= 0.367 Chirality : 0.048 0.348 1713 Planarity : 0.004 0.048 1860 Dihedral : 6.298 50.097 1692 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.61 % Allowed : 22.37 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.23), residues: 1357 helix: 0.22 (0.20), residues: 676 sheet: -1.92 (0.34), residues: 204 loop : -2.78 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 558 HIS 0.006 0.001 HIS A 802 PHE 0.028 0.002 PHE A 645 TYR 0.022 0.002 TYR A 810 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00874 ( 6) link_NAG-ASN : angle 4.76765 ( 18) link_BETA1-4 : bond 0.00611 ( 4) link_BETA1-4 : angle 3.16498 ( 12) hydrogen bonds : bond 0.04186 ( 531) hydrogen bonds : angle 4.88812 ( 1569) link_BETA1-6 : bond 0.00818 ( 1) link_BETA1-6 : angle 2.03293 ( 3) SS BOND : bond 0.00263 ( 7) SS BOND : angle 1.21477 ( 14) covalent geometry : bond 0.00296 (10874) covalent geometry : angle 0.74664 (14790) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4249.52 seconds wall clock time: 77 minutes 38.56 seconds (4658.56 seconds total)