Starting phenix.real_space_refine on Sat Jun 14 14:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.map" model { file = "/net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zks_60207/06_2025/8zks_60207.cif" } resolution = 3.21 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= 0.017 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 65 5.16 5 C 10459 2.51 5 N 2746 2.21 5 O 2899 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16170 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5402 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 29, 'TRANS': 701} Chain breaks: 5 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3959 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 11, 'TRANS': 468} Chain: "C" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3959 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 11, 'TRANS': 468} Chain: "D" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 2765 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 331} Link IDs: {'PTRANS': 11, 'TRANS': 469} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1286 Unresolved non-hydrogen angles: 1675 Unresolved non-hydrogen dihedrals: 1100 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 20, 'ASN:plan1': 20, 'TRP:plan': 9, 'ASP:plan': 15, 'PHE:plan': 31, 'GLU:plan': 20, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 755 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 9.60, per 1000 atoms: 0.59 Number of scatterers: 16170 At special positions: 0 Unit cell: (120.657, 164.137, 134.788, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 65 16.00 O 2899 8.00 N 2746 7.00 C 10459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A3770 " - pdb=" SG CYS A3811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " 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 NAG-ASN " NAG B1001 " - " ASN B 362 " " NAG B1002 " - " ASN B 375 " " NAG B1003 " - " ASN B 328 " " NAG C1002 " - " ASN C 375 " " NAG C1003 " - " ASN C 362 " " NAG C1004 " - " ASN C 328 " Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 2.1 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4120 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 54.6% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3101 removed outlier: 3.682A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A3093 " --> pdb=" O MET A3089 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A3094 " --> pdb=" O VAL A3090 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A3101 " --> pdb=" O LYS A3097 " (cutoff:3.500A) Processing helix chain 'A' and resid 3251 through 3256 removed outlier: 3.527A pdb=" N GLY A3256 " --> pdb=" O GLU A3252 " (cutoff:3.500A) Processing helix chain 'A' and resid 3261 through 3266 removed outlier: 3.891A pdb=" N LEU A3264 " --> pdb=" O HIS A3261 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3281 through 3301 removed outlier: 3.544A pdb=" N TRP A3298 " --> pdb=" O ALA A3294 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A3299 " --> pdb=" O ASN A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3320 through 3330 removed outlier: 4.314A pdb=" N GLY A3326 " --> pdb=" O THR A3322 " (cutoff:3.500A) Processing helix chain 'A' and resid 3333 through 3345 Processing helix chain 'A' and resid 3557 through 3578 removed outlier: 4.233A pdb=" N LEU A3563 " --> pdb=" O HIS A3559 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3617 removed outlier: 3.530A pdb=" N SER A3585 " --> pdb=" O PRO A3581 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) Proline residue: A3605 - end of helix Processing helix chain 'A' and resid 3655 through 3662 removed outlier: 3.534A pdb=" N ARG A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3689 removed outlier: 3.696A pdb=" N LEU A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) Processing helix chain 'A' and resid 3691 through 3709 Processing helix chain 'A' and resid 3710 through 3716 Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3731 through 3736 Processing helix chain 'A' and resid 3829 through 3838 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.970A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3926 Processing helix chain 'A' and resid 3933 through 3968 removed outlier: 4.098A pdb=" N LEU A3940 " --> pdb=" O TRP A3936 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A3949 " --> pdb=" O THR A3945 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4006 removed outlier: 3.938A pdb=" N ALA A3981 " --> pdb=" O PHE A3977 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN A3982 " --> pdb=" O ASP A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 4007 through 4009 No H-bonds generated for 'chain 'A' and resid 4007 through 4009' Processing helix chain 'A' and resid 4013 through 4041 removed outlier: 3.608A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A4018 " --> pdb=" O VAL A4014 " (cutoff:3.500A) Proline residue: A4024 - end of helix removed outlier: 3.584A pdb=" N LEU A4036 " --> pdb=" O GLY A4032 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A4040 " --> pdb=" O LEU A4036 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A4041 " --> pdb=" O GLY A4037 " (cutoff:3.500A) Processing helix chain 'A' and resid 4101 through 4119 removed outlier: 3.938A pdb=" N ILE A4105 " --> pdb=" O LEU A4101 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A4119 " --> pdb=" O GLY A4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 242 removed outlier: 3.631A pdb=" N THR B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 240 " --> pdb=" O ILE B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.526A pdb=" N ASP B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.583A pdb=" N LEU B 273 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.603A pdb=" N GLY B 290 " --> pdb=" O SER B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.734A pdb=" N LEU B 337 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 338' Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.710A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.942A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 498 removed outlier: 3.977A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.855A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 573 removed outlier: 3.850A pdb=" N ALA B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 570 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 571 " --> pdb=" O PHE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 removed outlier: 3.547A pdb=" N ILE B 577 " --> pdb=" O PHE B 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 580 through 620 removed outlier: 3.555A pdb=" N GLN B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 641 removed outlier: 3.641A pdb=" N ILE B 640 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 656 through 697 removed outlier: 3.594A pdb=" N TYR B 660 " --> pdb=" O LEU B 656 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 683 " --> pdb=" O ILE B 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 removed outlier: 3.784A pdb=" N SER C 243 " --> pdb=" O TYR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 259 Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.541A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 removed outlier: 3.688A pdb=" N GLU C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.548A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.733A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 removed outlier: 3.907A pdb=" N ALA C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 498 removed outlier: 3.788A pdb=" N PHE C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 473 " --> pdb=" O PHE C 469 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 474 " --> pdb=" O ASP C 470 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 537 removed outlier: 4.296A pdb=" N VAL C 512 " --> pdb=" O ASN C 508 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU C 533 " --> pdb=" O THR C 529 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL C 534 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 576 Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 594 through 620 removed outlier: 3.691A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 641 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.560A pdb=" N GLU C 650 " --> pdb=" O PHE C 646 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 695 removed outlier: 3.531A pdb=" N ILE C 680 " --> pdb=" O PHE C 676 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 242 Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 275 through 291 Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.570A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 370 through 374 removed outlier: 4.497A pdb=" N ASP D 373 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 492 removed outlier: 4.023A pdb=" N ILE D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 490 " --> pdb=" O TYR D 486 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.947A pdb=" N VAL D 515 " --> pdb=" O ASP D 511 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 516 " --> pdb=" O VAL D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 530 Processing helix chain 'D' and resid 550 through 577 Processing helix chain 'D' and resid 580 through 592 Processing helix chain 'D' and resid 593 through 620 removed outlier: 3.506A pdb=" N ALA D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 602 " --> pdb=" O PHE D 598 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 627 removed outlier: 3.665A pdb=" N SER D 627 " --> pdb=" O ASP D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.737A pdb=" N GLU D 650 " --> pdb=" O PHE D 646 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN D 653 " --> pdb=" O ILE D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 693 removed outlier: 3.805A pdb=" N LEU D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3138 through 3140 Processing sheet with id=AA2, first strand: chain 'A' and resid 3748 through 3749 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.610A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.625A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 322 through 324 886 hydrogen bonds defined for protein. 2592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 4.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2590 1.31 - 1.44: 4728 1.44 - 1.56: 9111 1.56 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 16529 Sorted by residual: bond pdb=" N ARG A3274 " pdb=" CA ARG A3274 " ideal model delta sigma weight residual 1.459 1.389 0.069 1.19e-02 7.06e+03 3.40e+01 bond pdb=" CA ARG A3274 " pdb=" C ARG A3274 " ideal model delta sigma weight residual 1.526 1.465 0.061 1.23e-02 6.61e+03 2.44e+01 bond pdb=" C1 NAG C1003 " pdb=" O5 NAG C1003 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C ARG A3274 " pdb=" O ARG A3274 " ideal model delta sigma weight residual 1.232 1.183 0.049 1.36e-02 5.41e+03 1.30e+01 bond pdb=" CA SER A3308 " pdb=" C SER A3308 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.18e+01 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 22339 2.59 - 5.17: 158 5.17 - 7.76: 23 7.76 - 10.34: 9 10.34 - 12.93: 4 Bond angle restraints: 22533 Sorted by residual: angle pdb=" N PHE A3275 " pdb=" CA PHE A3275 " pdb=" C PHE A3275 " ideal model delta sigma weight residual 109.54 99.48 10.06 1.37e+00 5.33e-01 5.39e+01 angle pdb=" C GLY A3310 " pdb=" N HIS A3311 " pdb=" CA HIS A3311 " ideal model delta sigma weight residual 124.82 111.89 12.93 1.78e+00 3.16e-01 5.28e+01 angle pdb=" CA ALA A3306 " pdb=" C ALA A3306 " pdb=" N TYR A3307 " ideal model delta sigma weight residual 118.08 108.60 9.48 1.31e+00 5.83e-01 5.24e+01 angle pdb=" N GLY A3310 " pdb=" CA GLY A3310 " pdb=" C GLY A3310 " ideal model delta sigma weight residual 112.73 120.58 -7.85 1.20e+00 6.94e-01 4.28e+01 angle pdb=" C ARG A3277 " pdb=" N ILE A3278 " pdb=" CA ILE A3278 " ideal model delta sigma weight residual 121.97 132.65 -10.68 1.80e+00 3.09e-01 3.52e+01 ... (remaining 22528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 9099 23.71 - 47.42: 535 47.42 - 71.12: 36 71.12 - 94.83: 9 94.83 - 118.54: 3 Dihedral angle restraints: 9682 sinusoidal: 3327 harmonic: 6355 Sorted by residual: dihedral pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " pdb=" SG CYS B 344 " pdb=" CB CYS B 344 " ideal model delta sinusoidal sigma weight residual 93.00 147.53 -54.53 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CA HIS B 501 " pdb=" C HIS B 501 " pdb=" N TYR B 502 " pdb=" CA TYR B 502 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLU C 312 " pdb=" C GLU C 312 " pdb=" N ASN C 313 " pdb=" CA ASN C 313 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2374 0.065 - 0.131: 239 0.131 - 0.196: 11 0.196 - 0.261: 2 0.261 - 0.326: 4 Chirality restraints: 2630 Sorted by residual: chirality pdb=" CA ILE A3278 " pdb=" N ILE A3278 " pdb=" C ILE A3278 " pdb=" CB ILE A3278 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA SER A3308 " pdb=" N SER A3308 " pdb=" C SER A3308 " pdb=" CB SER A3308 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ARG A3274 " pdb=" N ARG A3274 " pdb=" C ARG A3274 " pdb=" CB ARG A3274 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 2627 not shown) Planarity restraints: 2876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A3306 " -0.028 2.00e-02 2.50e+03 5.99e-02 3.59e+01 pdb=" C ALA A3306 " 0.103 2.00e-02 2.50e+03 pdb=" O ALA A3306 " -0.042 2.00e-02 2.50e+03 pdb=" N TYR A3307 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A3600 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C PHE A3600 " -0.046 2.00e-02 2.50e+03 pdb=" O PHE A3600 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A3601 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 309 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ILE D 309 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE D 309 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE D 310 " -0.013 2.00e-02 2.50e+03 ... (remaining 2873 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 68 2.53 - 3.13: 12401 3.13 - 3.72: 23946 3.72 - 4.31: 30997 4.31 - 4.90: 53628 Nonbonded interactions: 121040 Sorted by model distance: nonbonded pdb=" OG SER A3305 " pdb=" CB SER A3308 " model vdw 1.942 3.440 nonbonded pdb=" O SER A3305 " pdb=" N SER A3308 " model vdw 1.986 3.120 nonbonded pdb=" O ILE A3266 " pdb=" NE ARG A3277 " model vdw 2.060 3.120 nonbonded pdb=" NH2 ARG A3269 " pdb=" CG2 THR A3276 " model vdw 2.188 3.540 nonbonded pdb=" NH1 ARG A3848 " pdb=" O PHE A3873 " model vdw 2.241 3.120 ... (remaining 121035 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 'B' and ((resid 219 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 316 and (name N or name CA or name C or name O or name CB )) or resid 317 or \ (resid 318 through 328 and (name N or name CA or name C or name O or name CB )) \ or resid 329 or (resid 330 through 358 and (name N or name CA or name C or name \ O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (name \ N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 throu \ gh 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or \ (resid 382 through 387 and (name N or name CA or name C or name O or name CB )) \ or (resid 388 through 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (name \ N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 throug \ h 579 and (name N or name CA or name C or name O or name CB )) or resid 580 thro \ ugh 697)) selection = (chain 'C' and ((resid 219 through 239 and (name N or name CA or name C or name \ O or name CB )) or resid 240 or (resid 241 through 284 and (name N or name CA or \ name C or name O or name CB )) or resid 285 or (resid 286 through 289 and (name \ N or name CA or name C or name O or name CB )) or resid 290 or (resid 291 throu \ gh 316 and (name N or name CA or name C or name O or name CB )) or resid 317 or \ (resid 318 through 328 and (name N or name CA or name C or name O or name CB )) \ or resid 329 or (resid 330 through 358 and (name N or name CA or name C or name \ O or name CB )) or resid 359 or (resid 360 through 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 or (resid 364 through 375 and (name \ N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 throu \ gh 380 and (name N or name CA or name C or name O or name CB )) or resid 381 or \ (resid 382 through 387 and (name N or name CA or name C or name O or name CB )) \ or (resid 388 through 417 and (name N or name CA or name C or name O or name CB \ )) or resid 418 or (resid 419 through 448 and (name N or name CA or name C or na \ me O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (name \ N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 throug \ h 579 and (name N or name CA or name C or name O or name CB )) or resid 580 thro \ ugh 697)) selection = (chain 'D' and resid 219 through 697) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 36.930 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.003 0.080 16538 Z= 0.159 Angle : 0.610 12.930 22557 Z= 0.333 Chirality : 0.041 0.326 2630 Planarity : 0.004 0.060 2870 Dihedral : 14.037 118.539 5553 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.15 % Favored : 90.58 % Rotamer: Outliers : 0.14 % Allowed : 0.20 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 2154 helix: 2.09 (0.16), residues: 1030 sheet: -1.54 (0.39), residues: 188 loop : -2.78 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 293 HIS 0.004 0.001 HIS B 498 PHE 0.025 0.001 PHE C 538 TYR 0.023 0.001 TYR B 249 ARG 0.003 0.000 ARG B 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 6) link_NAG-ASN : angle 2.04976 ( 18) hydrogen bonds : bond 0.13196 ( 886) hydrogen bonds : angle 5.33901 ( 2592) SS BOND : bond 0.00193 ( 3) SS BOND : angle 1.20830 ( 6) covalent geometry : bond 0.00280 (16529) covalent geometry : angle 0.60701 (22533) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 1.649 Fit side-chains REVERT: A 3729 HIS cc_start: 0.8159 (t70) cc_final: 0.7893 (t-170) REVERT: C 542 GLN cc_start: 0.7077 (mp10) cc_final: 0.6621 (mp-120) REVERT: D 650 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8312 (tm-30) outliers start: 2 outliers final: 1 residues processed: 263 average time/residue: 0.2890 time to fit residues: 114.2127 Evaluate side-chains 221 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3278 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.0170 chunk 164 optimal weight: 0.0050 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 170 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 overall best weight: 0.8036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 636 GLN ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN C 578 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.170167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113917 restraints weight = 23272.111| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.46 r_work: 0.3178 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16538 Z= 0.115 Angle : 0.545 9.745 22557 Z= 0.282 Chirality : 0.039 0.215 2630 Planarity : 0.004 0.037 2870 Dihedral : 5.962 98.342 2467 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.64 % Favored : 91.18 % Rotamer: Outliers : 1.36 % Allowed : 7.07 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 2154 helix: 2.20 (0.16), residues: 1059 sheet: -1.53 (0.39), residues: 188 loop : -2.80 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 293 HIS 0.008 0.001 HIS B 498 PHE 0.023 0.001 PHE B 485 TYR 0.019 0.001 TYR B 249 ARG 0.011 0.000 ARG A3269 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 6) link_NAG-ASN : angle 2.18844 ( 18) hydrogen bonds : bond 0.04423 ( 886) hydrogen bonds : angle 4.40282 ( 2592) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.68181 ( 6) covalent geometry : bond 0.00237 (16529) covalent geometry : angle 0.54181 (22533) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 1.777 Fit side-chains REVERT: A 3274 ARG cc_start: 0.6730 (ptm160) cc_final: 0.6518 (ptt-90) REVERT: A 3325 VAL cc_start: 0.8784 (t) cc_final: 0.8545 (p) REVERT: A 3729 HIS cc_start: 0.8366 (t70) cc_final: 0.8119 (t-170) REVERT: B 603 MET cc_start: 0.8194 (mtp) cc_final: 0.7988 (mtp) REVERT: D 650 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8489 (tm-30) outliers start: 20 outliers final: 14 residues processed: 251 average time/residue: 0.2808 time to fit residues: 105.7871 Evaluate side-chains 240 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3100 GLN Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 571 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 89 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 135 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 177 optimal weight: 50.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3261 HIS ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 ASN D 681 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.162764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.104301 restraints weight = 23377.770| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.47 r_work: 0.3029 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16538 Z= 0.265 Angle : 0.656 9.940 22557 Z= 0.345 Chirality : 0.044 0.237 2630 Planarity : 0.004 0.040 2870 Dihedral : 6.056 96.242 2467 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.38 % Favored : 90.44 % Rotamer: Outliers : 2.11 % Allowed : 11.42 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2154 helix: 1.88 (0.16), residues: 1064 sheet: -1.90 (0.37), residues: 190 loop : -2.88 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 293 HIS 0.012 0.001 HIS B 498 PHE 0.024 0.002 PHE C 669 TYR 0.041 0.002 TYR B 249 ARG 0.004 0.000 ARG A3719 Details of bonding type rmsd link_NAG-ASN : bond 0.00372 ( 6) link_NAG-ASN : angle 2.35640 ( 18) hydrogen bonds : bond 0.06183 ( 886) hydrogen bonds : angle 4.61415 ( 2592) SS BOND : bond 0.00684 ( 3) SS BOND : angle 0.87780 ( 6) covalent geometry : bond 0.00646 (16529) covalent geometry : angle 0.65278 (22533) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.787 Fit side-chains REVERT: A 3267 TRP cc_start: 0.8049 (p90) cc_final: 0.7727 (p90) REVERT: A 3274 ARG cc_start: 0.6696 (ptm160) cc_final: 0.6462 (ptt-90) REVERT: A 4021 ARG cc_start: 0.9074 (tpp-160) cc_final: 0.8176 (tpt-90) REVERT: C 653 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8227 (t0) REVERT: D 650 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8577 (tm-30) outliers start: 31 outliers final: 25 residues processed: 239 average time/residue: 0.2887 time to fit residues: 103.1744 Evaluate side-chains 243 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 3975 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 582 THR Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 143 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 636 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109499 restraints weight = 23265.848| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.51 r_work: 0.3074 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16538 Z= 0.131 Angle : 0.549 10.101 22557 Z= 0.288 Chirality : 0.040 0.164 2630 Planarity : 0.003 0.038 2870 Dihedral : 5.585 87.394 2467 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.73 % Favored : 91.13 % Rotamer: Outliers : 2.58 % Allowed : 13.53 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.19), residues: 2154 helix: 2.17 (0.16), residues: 1054 sheet: -1.76 (0.38), residues: 188 loop : -2.86 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 293 HIS 0.003 0.001 HIS B 498 PHE 0.025 0.001 PHE B 485 TYR 0.025 0.001 TYR B 249 ARG 0.002 0.000 ARG A3712 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 6) link_NAG-ASN : angle 2.38288 ( 18) hydrogen bonds : bond 0.04826 ( 886) hydrogen bonds : angle 4.28711 ( 2592) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.66467 ( 6) covalent geometry : bond 0.00287 (16529) covalent geometry : angle 0.54493 (22533) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.766 Fit side-chains REVERT: A 3267 TRP cc_start: 0.8162 (p90) cc_final: 0.7928 (p90) REVERT: B 460 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8982 (pp) REVERT: C 259 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8883 (t0) REVERT: C 585 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7737 (tm-30) REVERT: D 650 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 693 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7468 (tm-30) outliers start: 38 outliers final: 27 residues processed: 253 average time/residue: 0.2863 time to fit residues: 108.5740 Evaluate side-chains 251 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3100 GLN Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 113 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 127 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3962 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 HIS B 636 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.163939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106748 restraints weight = 23594.893| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.56 r_work: 0.3044 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16538 Z= 0.195 Angle : 0.585 10.312 22557 Z= 0.308 Chirality : 0.041 0.161 2630 Planarity : 0.004 0.040 2870 Dihedral : 5.517 82.809 2467 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.56 % Favored : 90.30 % Rotamer: Outliers : 2.65 % Allowed : 15.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2154 helix: 2.04 (0.16), residues: 1065 sheet: -1.79 (0.38), residues: 190 loop : -2.89 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 293 HIS 0.004 0.001 HIS B 379 PHE 0.021 0.002 PHE A3600 TYR 0.031 0.002 TYR B 249 ARG 0.003 0.000 ARG B 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 6) link_NAG-ASN : angle 2.39582 ( 18) hydrogen bonds : bond 0.05318 ( 886) hydrogen bonds : angle 4.34002 ( 2592) SS BOND : bond 0.00493 ( 3) SS BOND : angle 0.66746 ( 6) covalent geometry : bond 0.00467 (16529) covalent geometry : angle 0.58137 (22533) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 232 time to evaluate : 1.756 Fit side-chains REVERT: A 3267 TRP cc_start: 0.8099 (p90) cc_final: 0.7760 (p90) REVERT: B 227 TYR cc_start: 0.8662 (t80) cc_final: 0.8298 (t80) REVERT: B 460 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8982 (pp) REVERT: B 605 PHE cc_start: 0.8134 (m-80) cc_final: 0.7643 (m-10) REVERT: C 259 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8849 (t0) REVERT: C 585 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7723 (tm-30) REVERT: D 650 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 693 GLN cc_start: 0.7629 (tm-30) cc_final: 0.7429 (tm-30) outliers start: 39 outliers final: 30 residues processed: 254 average time/residue: 0.2951 time to fit residues: 111.3919 Evaluate side-chains 255 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 293 TRP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain C residue 687 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 179 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 HIS B 636 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110739 restraints weight = 23338.821| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.46 r_work: 0.3106 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16538 Z= 0.113 Angle : 0.535 10.855 22557 Z= 0.280 Chirality : 0.039 0.159 2630 Planarity : 0.003 0.038 2870 Dihedral : 5.091 67.882 2467 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 2.11 % Allowed : 16.11 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2154 helix: 2.28 (0.16), residues: 1058 sheet: -1.67 (0.38), residues: 188 loop : -2.82 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 293 HIS 0.003 0.001 HIS A3261 PHE 0.030 0.001 PHE B 485 TYR 0.021 0.001 TYR B 249 ARG 0.004 0.000 ARG B 581 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 6) link_NAG-ASN : angle 2.56466 ( 18) hydrogen bonds : bond 0.04307 ( 886) hydrogen bonds : angle 4.11407 ( 2592) SS BOND : bond 0.00260 ( 3) SS BOND : angle 0.57115 ( 6) covalent geometry : bond 0.00235 (16529) covalent geometry : angle 0.53013 (22533) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 1.835 Fit side-chains REVERT: A 3729 HIS cc_start: 0.8348 (t70) cc_final: 0.8112 (t-170) REVERT: A 4021 ARG cc_start: 0.9020 (tpp-160) cc_final: 0.8125 (tpt-90) REVERT: B 460 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8960 (pp) REVERT: B 605 PHE cc_start: 0.8122 (m-80) cc_final: 0.7643 (m-10) REVERT: B 643 ASP cc_start: 0.8771 (t0) cc_final: 0.8503 (t0) REVERT: C 259 ASP cc_start: 0.9108 (OUTLIER) cc_final: 0.8834 (t0) REVERT: C 585 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7707 (tm-30) REVERT: D 650 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8549 (tm-30) outliers start: 31 outliers final: 22 residues processed: 243 average time/residue: 0.3038 time to fit residues: 111.5743 Evaluate side-chains 244 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 3883 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 16 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 188 optimal weight: 40.0000 chunk 84 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 22 optimal weight: 0.0670 chunk 145 optimal weight: 7.9990 chunk 132 optimal weight: 0.0010 chunk 55 optimal weight: 3.9990 overall best weight: 0.7326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 335 GLN B 498 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN D 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.168001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111366 restraints weight = 23357.476| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.47 r_work: 0.3113 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16538 Z= 0.109 Angle : 0.532 10.125 22557 Z= 0.276 Chirality : 0.039 0.156 2630 Planarity : 0.003 0.037 2870 Dihedral : 4.822 59.701 2467 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.31 % Favored : 91.55 % Rotamer: Outliers : 2.24 % Allowed : 16.93 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 2154 helix: 2.39 (0.16), residues: 1052 sheet: -1.51 (0.39), residues: 182 loop : -2.80 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 293 HIS 0.010 0.001 HIS B 498 PHE 0.018 0.001 PHE A3600 TYR 0.019 0.001 TYR B 249 ARG 0.005 0.000 ARG A3712 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 6) link_NAG-ASN : angle 2.76875 ( 18) hydrogen bonds : bond 0.04098 ( 886) hydrogen bonds : angle 4.06126 ( 2592) SS BOND : bond 0.00230 ( 3) SS BOND : angle 0.53691 ( 6) covalent geometry : bond 0.00226 (16529) covalent geometry : angle 0.52633 (22533) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.710 Fit side-chains REVERT: A 3729 HIS cc_start: 0.8338 (t70) cc_final: 0.8091 (t-170) REVERT: A 4021 ARG cc_start: 0.9019 (tpp-160) cc_final: 0.8184 (tpt-90) REVERT: B 338 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7963 (ttm170) REVERT: B 643 ASP cc_start: 0.8782 (t0) cc_final: 0.8492 (t0) REVERT: C 259 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8753 (t0) REVERT: C 585 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 650 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8560 (tm-30) outliers start: 33 outliers final: 26 residues processed: 243 average time/residue: 0.2793 time to fit residues: 101.1517 Evaluate side-chains 252 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 128 optimal weight: 0.0270 chunk 147 optimal weight: 0.9980 chunk 199 optimal weight: 50.0000 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 179 optimal weight: 50.0000 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3100 GLN B 335 GLN B 498 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110556 restraints weight = 23202.956| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.45 r_work: 0.3103 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16538 Z= 0.123 Angle : 0.535 9.789 22557 Z= 0.278 Chirality : 0.039 0.154 2630 Planarity : 0.003 0.038 2870 Dihedral : 4.676 59.556 2467 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.45 % Favored : 91.41 % Rotamer: Outliers : 2.45 % Allowed : 16.79 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 2154 helix: 2.38 (0.16), residues: 1050 sheet: -1.50 (0.39), residues: 182 loop : -2.76 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 293 HIS 0.003 0.001 HIS B 498 PHE 0.032 0.001 PHE B 485 TYR 0.021 0.001 TYR B 249 ARG 0.004 0.000 ARG A3712 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 6) link_NAG-ASN : angle 2.88967 ( 18) hydrogen bonds : bond 0.04219 ( 886) hydrogen bonds : angle 4.05766 ( 2592) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.51498 ( 6) covalent geometry : bond 0.00275 (16529) covalent geometry : angle 0.52872 (22533) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 230 time to evaluate : 1.754 Fit side-chains REVERT: A 3729 HIS cc_start: 0.8343 (t70) cc_final: 0.8088 (t-170) REVERT: A 3744 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8644 (tt) REVERT: A 4021 ARG cc_start: 0.9019 (tpp-160) cc_final: 0.8175 (tpt-90) REVERT: B 338 ARG cc_start: 0.8308 (ttm170) cc_final: 0.7957 (ttm170) REVERT: B 460 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8969 (pp) REVERT: B 605 PHE cc_start: 0.8189 (m-80) cc_final: 0.7657 (m-10) REVERT: B 643 ASP cc_start: 0.8791 (t0) cc_final: 0.8490 (t0) REVERT: C 259 ASP cc_start: 0.9005 (OUTLIER) cc_final: 0.8746 (t0) REVERT: C 585 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7719 (tm-30) REVERT: D 650 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8564 (tm-30) outliers start: 36 outliers final: 29 residues processed: 249 average time/residue: 0.2840 time to fit residues: 105.5974 Evaluate side-chains 260 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 18 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 196 optimal weight: 50.0000 chunk 66 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 200 optimal weight: 50.0000 chunk 132 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3100 GLN B 498 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN D 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110944 restraints weight = 23314.315| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.44 r_work: 0.3112 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16538 Z= 0.115 Angle : 0.529 9.791 22557 Z= 0.276 Chirality : 0.039 0.155 2630 Planarity : 0.003 0.038 2870 Dihedral : 4.561 58.461 2467 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.50 % Favored : 91.36 % Rotamer: Outliers : 2.58 % Allowed : 16.59 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2154 helix: 2.42 (0.16), residues: 1051 sheet: -1.49 (0.39), residues: 182 loop : -2.76 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 293 HIS 0.010 0.001 HIS B 498 PHE 0.019 0.001 PHE A3600 TYR 0.019 0.001 TYR B 249 ARG 0.003 0.000 ARG A3712 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 6) link_NAG-ASN : angle 2.78268 ( 18) hydrogen bonds : bond 0.04093 ( 886) hydrogen bonds : angle 4.03201 ( 2592) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.50669 ( 6) covalent geometry : bond 0.00248 (16529) covalent geometry : angle 0.52358 (22533) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.971 Fit side-chains REVERT: A 3729 HIS cc_start: 0.8336 (t70) cc_final: 0.8069 (t-170) REVERT: A 3744 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8614 (tt) REVERT: A 4021 ARG cc_start: 0.9026 (tpp-160) cc_final: 0.8181 (tpt-90) REVERT: B 338 ARG cc_start: 0.8269 (ttm170) cc_final: 0.7917 (ttm170) REVERT: B 460 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8966 (pp) REVERT: B 605 PHE cc_start: 0.8188 (m-80) cc_final: 0.7646 (m-10) REVERT: B 643 ASP cc_start: 0.8790 (t0) cc_final: 0.8492 (t0) REVERT: C 259 ASP cc_start: 0.8987 (OUTLIER) cc_final: 0.8744 (t0) REVERT: C 585 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 650 GLU cc_start: 0.9006 (tm-30) cc_final: 0.8550 (tm-30) outliers start: 38 outliers final: 32 residues processed: 255 average time/residue: 0.2974 time to fit residues: 112.3659 Evaluate side-chains 264 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 229 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 335 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 498 HIS Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 693 GLN Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 202 optimal weight: 50.0000 chunk 19 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 201 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3100 GLN B 335 GLN B 498 HIS ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110929 restraints weight = 23362.773| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.43 r_work: 0.3112 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16538 Z= 0.118 Angle : 0.532 9.796 22557 Z= 0.278 Chirality : 0.039 0.159 2630 Planarity : 0.003 0.038 2870 Dihedral : 4.504 58.479 2467 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 2.52 % Allowed : 17.13 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.19), residues: 2154 helix: 2.39 (0.16), residues: 1055 sheet: -1.49 (0.39), residues: 182 loop : -2.76 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 293 HIS 0.006 0.001 HIS B 498 PHE 0.033 0.001 PHE B 485 TYR 0.020 0.001 TYR B 249 ARG 0.003 0.000 ARG A4100 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 6) link_NAG-ASN : angle 2.63359 ( 18) hydrogen bonds : bond 0.04113 ( 886) hydrogen bonds : angle 4.03292 ( 2592) SS BOND : bond 0.00276 ( 3) SS BOND : angle 0.53891 ( 6) covalent geometry : bond 0.00261 (16529) covalent geometry : angle 0.52712 (22533) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 1.745 Fit side-chains REVERT: A 3611 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 3729 HIS cc_start: 0.8340 (t70) cc_final: 0.8069 (t-170) REVERT: A 3744 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8607 (tt) REVERT: A 4021 ARG cc_start: 0.9023 (tpp-160) cc_final: 0.8174 (tpt-90) REVERT: B 460 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 643 ASP cc_start: 0.8771 (t0) cc_final: 0.8531 (t0) REVERT: C 259 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8730 (t0) REVERT: C 585 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 650 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8547 (tm-30) outliers start: 37 outliers final: 28 residues processed: 256 average time/residue: 0.2933 time to fit residues: 111.8629 Evaluate side-chains 265 residues out of total 1896 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3278 ILE Chi-restraints excluded: chain A residue 3331 VAL Chi-restraints excluded: chain A residue 3336 VAL Chi-restraints excluded: chain A residue 3601 LEU Chi-restraints excluded: chain A residue 3610 LEU Chi-restraints excluded: chain A residue 3707 GLN Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3754 LEU Chi-restraints excluded: chain A residue 4004 GLN Chi-restraints excluded: chain A residue 4113 LEU Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 427 SER Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 542 GLN Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 697 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 210 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 119 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3100 GLN ** C 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.163810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106498 restraints weight = 23385.192| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.40 r_work: 0.3047 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16538 Z= 0.204 Angle : 0.593 9.900 22557 Z= 0.313 Chirality : 0.042 0.160 2630 Planarity : 0.004 0.038 2870 Dihedral : 4.714 53.928 2467 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 2.38 % Allowed : 17.13 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 2154 helix: 2.11 (0.16), residues: 1069 sheet: -1.76 (0.38), residues: 190 loop : -2.81 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 293 HIS 0.004 0.001 HIS C 379 PHE 0.022 0.002 PHE A3600 TYR 0.025 0.002 TYR B 249 ARG 0.004 0.000 ARG A3712 Details of bonding type rmsd link_NAG-ASN : bond 0.00259 ( 6) link_NAG-ASN : angle 2.49834 ( 18) hydrogen bonds : bond 0.05376 ( 886) hydrogen bonds : angle 4.26118 ( 2592) SS BOND : bond 0.00529 ( 3) SS BOND : angle 0.65090 ( 6) covalent geometry : bond 0.00485 (16529) covalent geometry : angle 0.58922 (22533) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9371.00 seconds wall clock time: 160 minutes 49.20 seconds (9649.20 seconds total)