Starting phenix.real_space_refine on Thu Feb 5 09:10:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0w_62726/02_2026/9l0w_62726.map" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 10388 2.51 5 N 2727 2.21 5 O 2849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16028 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 5474 Classifications: {'peptide': 739} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 28, 'TRANS': 710} 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: {'ARG:plan': 10, 'PHE:plan': 6, 'TYR:plan': 2, 'GLU:plan': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3932 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3860 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 10, 'TRANS': 457} Chain breaks: 1 Chain: "D" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 2678 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'PTRANS': 10, 'TRANS': 462} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1315 Unresolved non-hydrogen angles: 1709 Unresolved non-hydrogen dihedrals: 1126 Unresolved non-hydrogen chiralities: 121 Planarities with less than four sites: {'TYR:plan': 21, 'ARG:plan': 21, 'GLU:plan': 19, 'PHE:plan': 31, 'ASN:plan1': 20, 'GLN:plan1': 12, 'ASP:plan': 14, 'TRP:plan': 9, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 765 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: 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 Time building chain proxies: 3.79, per 1000 atoms: 0.24 Number of scatterers: 16028 At special positions: 0 Unit cell: (125.005, 158.702, 132.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 2849 8.00 N 2727 7.00 C 10388 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=2.02 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 375 " " NAG B1002 " - " ASN B 362 " " NAG B1003 " - " ASN B 328 " " NAG C1001 " - " ASN C 375 " " NAG C1002 " - " ASN C 362 " " NAG C1003 " - " ASN C 328 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 740.0 milliseconds 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4088 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 6 sheets defined 55.6% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3106 removed outlier: 4.273A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A3097 " --> pdb=" O ALA A3093 " (cutoff:3.500A) Processing helix chain 'A' and resid 3247 through 3257 Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.687A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3262 through 3266' Processing helix chain 'A' and resid 3278 through 3299 removed outlier: 3.612A pdb=" N THR A3282 " --> pdb=" O ILE A3278 " (cutoff:3.500A) Processing helix chain 'A' and resid 3322 through 3334 removed outlier: 3.987A pdb=" N TYR A3334 " --> pdb=" O SER A3330 " (cutoff:3.500A) Processing helix chain 'A' and resid 3337 through 3345 Processing helix chain 'A' and resid 3553 through 3577 removed outlier: 4.109A pdb=" N LEU A3557 " --> pdb=" O TRP A3553 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A3559 " --> pdb=" O ALA A3555 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY A3560 " --> pdb=" O SER A3556 " (cutoff:3.500A) Processing helix chain 'A' and resid 3578 through 3580 No H-bonds generated for 'chain 'A' and resid 3578 through 3580' Processing helix chain 'A' and resid 3581 through 3599 removed outlier: 4.091A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) Processing helix chain 'A' and resid 3602 through 3618 removed outlier: 3.830A pdb=" N LEU A3606 " --> pdb=" O GLY A3602 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A3618 " --> pdb=" O TYR A3614 " (cutoff:3.500A) Processing helix chain 'A' and resid 3656 through 3690 removed outlier: 3.697A pdb=" N LEU A3675 " --> pdb=" O LEU A3671 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A3676 " --> pdb=" O ARG A3672 " (cutoff:3.500A) Processing helix chain 'A' and resid 3694 through 3709 Processing helix chain 'A' and resid 3710 through 3717 removed outlier: 3.657A pdb=" N ILE A3717 " --> pdb=" O ALA A3713 " (cutoff:3.500A) Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3731 through 3736 Processing helix chain 'A' and resid 3826 through 3839 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.690A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3904 Processing helix chain 'A' and resid 3905 through 3926 removed outlier: 3.841A pdb=" N ARG A3924 " --> pdb=" O ARG A3920 " (cutoff:3.500A) Processing helix chain 'A' and resid 3932 through 3969 removed outlier: 3.747A pdb=" N ARG A3938 " --> pdb=" O GLY A3934 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N TRP A3939 " --> pdb=" O ALA A3935 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A3941 " --> pdb=" O ALA A3937 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL A3942 " --> pdb=" O ARG A3938 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A3952 " --> pdb=" O THR A3948 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A3953 " --> pdb=" O ALA A3949 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4005 removed outlier: 3.574A pdb=" N ARG A3988 " --> pdb=" O SER A3984 " (cutoff:3.500A) Processing helix chain 'A' and resid 4006 through 4009 removed outlier: 3.686A pdb=" N VAL A4009 " --> pdb=" O LEU A4006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4006 through 4009' Processing helix chain 'A' and resid 4013 through 4037 removed outlier: 3.832A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) Proline residue: A4024 - end of helix Processing helix chain 'A' and resid 4101 through 4118 removed outlier: 3.643A pdb=" N ILE A4105 " --> pdb=" O LEU A4101 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 241 removed outlier: 3.552A pdb=" N TYR B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 259 removed outlier: 4.125A pdb=" N TYR B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 284 removed outlier: 3.612A pdb=" N GLU B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.924A pdb=" N GLU B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.530A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 Processing helix chain 'B' and resid 398 through 412 removed outlier: 3.971A pdb=" N ALA B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 495 removed outlier: 3.698A pdb=" N GLU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 531 removed outlier: 3.568A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 541 removed outlier: 3.512A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 541 " --> pdb=" O GLN B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 removed outlier: 3.524A pdb=" N VAL B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 593 through 620 removed outlier: 3.533A pdb=" N ILE B 602 " --> pdb=" O PHE B 598 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 641 Processing helix chain 'B' and resid 655 through 670 removed outlier: 3.867A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 698 removed outlier: 4.326A pdb=" N ALA B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 241 removed outlier: 3.528A pdb=" N VAL C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 259 removed outlier: 3.965A pdb=" N TYR C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.925A pdb=" N LEU C 273 " --> pdb=" O PHE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 285 through 292 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.535A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 468 through 496 removed outlier: 3.675A pdb=" N PHE C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.803A pdb=" N ASN C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.879A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 537 " --> pdb=" O GLU C 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 537' Processing helix chain 'C' and resid 548 through 572 removed outlier: 3.558A pdb=" N PHE C 558 " --> pdb=" O TRP C 554 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN C 559 " --> pdb=" O GLN C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 580 through 593 removed outlier: 3.624A pdb=" N CYS C 593 " --> pdb=" O THR C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 619 removed outlier: 3.735A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 Processing helix chain 'C' and resid 648 through 653 Processing helix chain 'C' and resid 656 through 671 removed outlier: 3.562A pdb=" N TYR C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 698 removed outlier: 3.832A pdb=" N MET C 675 " --> pdb=" O ILE C 671 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C 676 " --> pdb=" O LEU C 672 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 698 " --> pdb=" O GLN C 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 240 removed outlier: 4.451A pdb=" N GLU D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 224 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.739A pdb=" N GLU D 353 " --> pdb=" O VAL D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 412 removed outlier: 3.591A pdb=" N ALA D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 494 removed outlier: 3.884A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 536 removed outlier: 4.147A pdb=" N ASP D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 577 removed outlier: 3.568A pdb=" N GLN D 557 " --> pdb=" O TYR D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 580 No H-bonds generated for 'chain 'D' and resid 578 through 580' Processing helix chain 'D' and resid 597 through 619 removed outlier: 3.753A pdb=" N MET D 603 " --> pdb=" O GLY D 599 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 642 removed outlier: 3.725A pdb=" N PHE D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 656 through 670 removed outlier: 3.566A pdb=" N TYR D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 695 removed outlier: 4.066A pdb=" N ALA D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA D 678 " --> pdb=" O ASN D 674 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE D 680 " --> pdb=" O PHE D 676 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3137 through 3140 Processing sheet with id=AA2, first strand: chain 'A' and resid 3196 through 3197 removed outlier: 3.581A pdb=" N LEU A3197 " --> pdb=" O ASP A3217 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A3217 " --> pdb=" O LEU A3197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 3748 through 3749 removed outlier: 3.571A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ARG A3878 " --> pdb=" O PRO A3874 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 7.022A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.490A pdb=" N LEU C 316 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL C 428 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N VAL C 318 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE C 426 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE C 426 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 394 removed outlier: 3.844A pdb=" N GLU D 444 " --> pdb=" O ILE D 452 " (cutoff:3.500A) 913 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5172 1.34 - 1.47: 4287 1.47 - 1.59: 6827 1.59 - 1.71: 0 1.71 - 1.83: 97 Bond restraints: 16383 Sorted by residual: bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C3 NAG C1001 " pdb=" O3 NAG C1001 " ideal model delta sigma weight residual 1.403 1.433 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 NAG C1003 " pdb=" O5 NAG C1003 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" C5 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG B1003 " pdb=" O5 NAG B1003 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.93e+00 ... (remaining 16378 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22010 2.24 - 4.48: 267 4.48 - 6.72: 38 6.72 - 8.96: 8 8.96 - 11.20: 1 Bond angle restraints: 22324 Sorted by residual: angle pdb=" C ALA D 594 " pdb=" N LYS D 595 " pdb=" CA LYS D 595 " ideal model delta sigma weight residual 122.44 117.71 4.73 1.19e+00 7.06e-01 1.58e+01 angle pdb=" CA ASN C 578 " pdb=" C ASN C 578 " pdb=" N PHE C 579 " ideal model delta sigma weight residual 118.27 124.38 -6.11 1.59e+00 3.96e-01 1.48e+01 angle pdb=" N THR A3769 " pdb=" CA THR A3769 " pdb=" C THR A3769 " ideal model delta sigma weight residual 114.64 108.97 5.67 1.52e+00 4.33e-01 1.39e+01 angle pdb=" N ILE C 463 " pdb=" CA ILE C 463 " pdb=" C ILE C 463 " ideal model delta sigma weight residual 111.48 108.07 3.41 9.40e-01 1.13e+00 1.32e+01 angle pdb=" N SER D 274 " pdb=" CA SER D 274 " pdb=" C SER D 274 " ideal model delta sigma weight residual 114.56 109.99 4.57 1.27e+00 6.20e-01 1.29e+01 ... (remaining 22319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.81: 9022 22.81 - 45.62: 508 45.62 - 68.42: 40 68.42 - 91.23: 14 91.23 - 114.04: 3 Dihedral angle restraints: 9587 sinusoidal: 3282 harmonic: 6305 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 -177.05 -89.95 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CA ARG A4100 " pdb=" C ARG A4100 " pdb=" N LEU A4101 " pdb=" CA LEU A4101 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ALA D 594 " pdb=" C ALA D 594 " pdb=" N LYS D 595 " pdb=" CA LYS D 595 " ideal model delta harmonic sigma weight residual 180.00 156.88 23.12 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 9584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.162: 2605 0.162 - 0.323: 3 0.323 - 0.485: 0 0.485 - 0.647: 0 0.647 - 0.809: 1 Chirality restraints: 2609 Sorted by residual: chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 375 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 375 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE C 497 " pdb=" N ILE C 497 " pdb=" C ILE C 497 " pdb=" CB ILE C 497 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 2606 not shown) Planarity restraints: 2836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1001 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG C1001 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C1001 " 0.055 2.00e-02 2.50e+03 pdb=" N2 NAG C1001 " -0.517 2.00e-02 2.50e+03 pdb=" O7 NAG C1001 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 375 " -0.235 2.00e-02 2.50e+03 2.28e-01 6.52e+02 pdb=" CG ASN C 375 " 0.080 2.00e-02 2.50e+03 pdb=" OD1 ASN C 375 " 0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN C 375 " 0.348 2.00e-02 2.50e+03 pdb=" C1 NAG C1001 " -0.268 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A3842 " -0.022 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A3842 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP A3842 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A3842 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A3842 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A3842 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A3842 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A3842 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A3842 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A3842 " 0.002 2.00e-02 2.50e+03 ... (remaining 2833 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1269 2.74 - 3.28: 16304 3.28 - 3.82: 25972 3.82 - 4.36: 27204 4.36 - 4.90: 48722 Nonbonded interactions: 119471 Sorted by model distance: nonbonded pdb=" O ILE A3266 " pdb=" NH1 ARG A3277 " model vdw 2.201 3.120 nonbonded pdb=" OE2 GLU B 343 " pdb=" NH2 ARG B 417 " model vdw 2.235 3.120 nonbonded pdb=" O PRO A3725 " pdb=" ND1 HIS A3729 " model vdw 2.245 3.120 nonbonded pdb=" OG1 THR C 265 " pdb=" OE1 GLU C 266 " model vdw 2.263 3.040 nonbonded pdb=" CG ARG A3766 " pdb=" NH2 ARG A3878 " model vdw 2.268 3.520 ... (remaining 119466 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 215 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 294 and (name N or name CA or name C or name O or name CB )) or (resid 311 th \ rough 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 na \ me 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 376 or (resid 377 th \ rough 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 \ name O or name CB )) or resid 449 through 450 or (resid 451 through 522 and (na \ me N or name CA or name C or name O or name CB )) or resid 523 or (resid 524 thr \ ough 592 and (name N or name CA or name C or name O or name CB )) or resid 593 t \ hrough 695)) selection = (chain 'C' and ((resid 215 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 592 and (name N or name CA or name C or name O or name CB )) or resid 593 thro \ ugh 695)) selection = (chain 'D' and (resid 215 through 294 or resid 311 through 695)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.500 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.004 0.319 16392 Z= 0.190 Angle : 0.714 38.327 22348 Z= 0.368 Chirality : 0.043 0.809 2609 Planarity : 0.006 0.294 2830 Dihedral : 13.841 114.039 5490 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.82 % Rotamer: Outliers : 0.07 % Allowed : 0.35 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.19), residues: 2132 helix: 1.60 (0.16), residues: 1113 sheet: -0.63 (0.39), residues: 196 loop : -2.98 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 654 TYR 0.021 0.001 TYR B 502 PHE 0.015 0.001 PHE C 436 TRP 0.062 0.002 TRP A3842 HIS 0.005 0.001 HIS A3729 Details of bonding type rmsd covalent geometry : bond 0.00270 (16383) covalent geometry : angle 0.63332 (22324) SS BOND : bond 0.00464 ( 3) SS BOND : angle 3.00253 ( 6) hydrogen bonds : bond 0.15666 ( 913) hydrogen bonds : angle 5.39039 ( 2664) link_NAG-ASN : bond 0.13010 ( 6) link_NAG-ASN : angle 11.54495 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 583 MET cc_start: 0.7969 (mmm) cc_final: 0.7559 (mmm) REVERT: B 669 PHE cc_start: 0.7076 (t80) cc_final: 0.6837 (t80) REVERT: B 690 ASP cc_start: 0.8526 (m-30) cc_final: 0.8207 (m-30) REVERT: C 238 THR cc_start: 0.8882 (p) cc_final: 0.8528 (p) REVERT: C 686 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 687 VAL cc_start: 0.8946 (t) cc_final: 0.8649 (p) REVERT: D 673 LEU cc_start: 0.8966 (mt) cc_final: 0.8589 (tt) outliers start: 1 outliers final: 0 residues processed: 382 average time/residue: 0.1330 time to fit residues: 75.5073 Evaluate side-chains 239 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 ASN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 674 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.085037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062855 restraints weight = 79266.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.063811 restraints weight = 52553.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.064409 restraints weight = 39307.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.064880 restraints weight = 32989.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.065416 restraints weight = 28888.637| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16392 Z= 0.129 Angle : 0.700 17.658 22348 Z= 0.337 Chirality : 0.043 0.239 2609 Planarity : 0.004 0.040 2830 Dihedral : 6.299 99.959 2447 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 1.73 % Allowed : 12.74 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 2132 helix: 1.88 (0.16), residues: 1104 sheet: -0.39 (0.40), residues: 194 loop : -2.82 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 592 TYR 0.012 0.001 TYR C 611 PHE 0.024 0.001 PHE C 480 TRP 0.017 0.001 TRP A3842 HIS 0.003 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00275 (16383) covalent geometry : angle 0.69651 (22324) SS BOND : bond 0.00234 ( 3) SS BOND : angle 1.88165 ( 6) hydrogen bonds : bond 0.04112 ( 913) hydrogen bonds : angle 4.22301 ( 2664) link_NAG-ASN : bond 0.00545 ( 6) link_NAG-ASN : angle 2.23851 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 268 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4001 LYS cc_start: 0.9270 (tppt) cc_final: 0.9029 (tptp) REVERT: A 4017 LYS cc_start: 0.9641 (ptpp) cc_final: 0.9422 (ptpp) REVERT: A 4096 TRP cc_start: 0.5630 (m100) cc_final: 0.5337 (m100) REVERT: A 4108 TRP cc_start: 0.8671 (t60) cc_final: 0.8432 (t60) REVERT: B 583 MET cc_start: 0.9519 (mmm) cc_final: 0.9225 (mmp) REVERT: B 624 ASP cc_start: 0.8155 (m-30) cc_final: 0.7878 (t0) REVERT: B 686 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8384 (tm-30) REVERT: B 690 ASP cc_start: 0.9212 (m-30) cc_final: 0.8623 (m-30) REVERT: C 252 MET cc_start: 0.8292 (ptm) cc_final: 0.7928 (ptm) REVERT: C 440 ARG cc_start: 0.9154 (tpp80) cc_final: 0.8637 (tpp80) REVERT: C 603 MET cc_start: 0.9174 (mtm) cc_final: 0.8952 (ptp) REVERT: C 697 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 613 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8571 (tp-100) outliers start: 25 outliers final: 11 residues processed: 279 average time/residue: 0.1199 time to fit residues: 51.8428 Evaluate side-chains 246 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 0.0980 chunk 200 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.079109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057695 restraints weight = 77135.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058456 restraints weight = 50876.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.059166 restraints weight = 39083.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059730 restraints weight = 32042.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.059905 restraints weight = 27503.861| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16392 Z= 0.217 Angle : 0.699 14.572 22348 Z= 0.350 Chirality : 0.044 0.267 2609 Planarity : 0.004 0.042 2830 Dihedral : 6.092 93.374 2447 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 3.46 % Allowed : 16.07 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 2132 helix: 1.86 (0.16), residues: 1116 sheet: -0.28 (0.40), residues: 189 loop : -2.84 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 592 TYR 0.015 0.002 TYR D 684 PHE 0.015 0.001 PHE C 472 TRP 0.016 0.001 TRP A3842 HIS 0.005 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00465 (16383) covalent geometry : angle 0.69676 (22324) SS BOND : bond 0.00397 ( 3) SS BOND : angle 0.89345 ( 6) hydrogen bonds : bond 0.04137 ( 913) hydrogen bonds : angle 4.11704 ( 2664) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 2.18737 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3897 LEU cc_start: 0.9218 (tp) cc_final: 0.8941 (tt) REVERT: A 4108 TRP cc_start: 0.8884 (t60) cc_final: 0.8592 (t60) REVERT: B 251 ARG cc_start: 0.9271 (ptm160) cc_final: 0.8512 (tmm-80) REVERT: B 252 MET cc_start: 0.9008 (mmm) cc_final: 0.7201 (mmm) REVERT: B 425 ASP cc_start: 0.8174 (p0) cc_final: 0.7947 (p0) REVERT: B 444 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 252 MET cc_start: 0.7853 (ptm) cc_final: 0.7629 (ptm) REVERT: C 631 GLU cc_start: 0.9614 (tp30) cc_final: 0.9182 (tp30) REVERT: C 693 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8905 (tp-100) REVERT: D 613 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8572 (tp-100) REVERT: D 629 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: D 675 MET cc_start: 0.9671 (OUTLIER) cc_final: 0.9294 (ppp) outliers start: 50 outliers final: 31 residues processed: 256 average time/residue: 0.1175 time to fit residues: 46.7754 Evaluate side-chains 228 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3262 ILE Chi-restraints excluded: chain A residue 3268 ASP Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3290 LEU Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3597 LEU Chi-restraints excluded: chain A residue 3675 LEU Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain A residue 3941 LEU Chi-restraints excluded: chain A residue 4000 VAL Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain B residue 688 LYS Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 31 optimal weight: 8.9990 chunk 199 optimal weight: 50.0000 chunk 207 optimal weight: 4.9990 chunk 203 optimal weight: 0.0570 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 172 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 178 optimal weight: 0.0770 chunk 26 optimal weight: 0.0980 overall best weight: 1.2460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 578 ASN ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.080247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059001 restraints weight = 80240.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.059948 restraints weight = 51746.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.060483 restraints weight = 38139.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060907 restraints weight = 31445.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061355 restraints weight = 27320.002| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16392 Z= 0.117 Angle : 0.669 13.524 22348 Z= 0.317 Chirality : 0.042 0.301 2609 Planarity : 0.003 0.064 2830 Dihedral : 5.846 86.070 2447 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 2.56 % Allowed : 18.84 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2132 helix: 2.01 (0.16), residues: 1111 sheet: -0.10 (0.40), residues: 189 loop : -2.75 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A3712 TYR 0.015 0.001 TYR D 684 PHE 0.027 0.001 PHE C 480 TRP 0.013 0.001 TRP B 570 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00251 (16383) covalent geometry : angle 0.66628 (22324) SS BOND : bond 0.00662 ( 3) SS BOND : angle 1.22213 ( 6) hydrogen bonds : bond 0.03592 ( 913) hydrogen bonds : angle 3.87567 ( 2664) link_NAG-ASN : bond 0.00275 ( 6) link_NAG-ASN : angle 1.99774 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4101 LEU cc_start: 0.9401 (tt) cc_final: 0.8982 (mt) REVERT: A 4108 TRP cc_start: 0.8722 (t60) cc_final: 0.8302 (t60) REVERT: B 251 ARG cc_start: 0.9279 (ptm160) cc_final: 0.8653 (tmm-80) REVERT: B 252 MET cc_start: 0.9021 (mmm) cc_final: 0.8767 (mmm) REVERT: B 425 ASP cc_start: 0.8016 (p0) cc_final: 0.7800 (p0) REVERT: B 444 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7772 (mt-10) REVERT: B 631 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8862 (tt0) REVERT: B 686 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8825 (tm-30) REVERT: C 252 MET cc_start: 0.7721 (ptm) cc_final: 0.7476 (ptm) REVERT: C 440 ARG cc_start: 0.9283 (tpp80) cc_final: 0.8923 (tpp80) REVERT: C 675 MET cc_start: 0.9432 (mmm) cc_final: 0.9080 (mmm) REVERT: C 693 GLN cc_start: 0.9125 (tp-100) cc_final: 0.8129 (tp-100) REVERT: C 697 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7663 (mm-30) REVERT: D 613 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8415 (tp-100) REVERT: D 629 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7863 (m-80) outliers start: 37 outliers final: 19 residues processed: 252 average time/residue: 0.1162 time to fit residues: 45.7198 Evaluate side-chains 226 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3268 ASP Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3709 LEU Chi-restraints excluded: chain A residue 3871 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 487 TYR Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 656 LEU Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 0.0020 chunk 212 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN C 379 HIS D 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.081514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.060003 restraints weight = 76200.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.060706 restraints weight = 52695.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061286 restraints weight = 37610.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061770 restraints weight = 30609.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062003 restraints weight = 26268.087| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 16392 Z= 0.111 Angle : 0.659 13.322 22348 Z= 0.311 Chirality : 0.042 0.253 2609 Planarity : 0.003 0.046 2830 Dihedral : 5.383 74.692 2447 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 2.22 % Allowed : 20.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.19), residues: 2132 helix: 2.01 (0.16), residues: 1109 sheet: -0.16 (0.40), residues: 194 loop : -2.74 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3712 TYR 0.016 0.001 TYR D 684 PHE 0.013 0.001 PHE D 666 TRP 0.014 0.001 TRP B 570 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00240 (16383) covalent geometry : angle 0.65742 (22324) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.77034 ( 6) hydrogen bonds : bond 0.03382 ( 913) hydrogen bonds : angle 3.77733 ( 2664) link_NAG-ASN : bond 0.00224 ( 6) link_NAG-ASN : angle 1.89986 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8425 (pp) REVERT: A 3290 LEU cc_start: 0.9707 (mm) cc_final: 0.9323 (tp) REVERT: A 3678 MET cc_start: 0.9043 (mmm) cc_final: 0.8743 (mmm) REVERT: A 4017 LYS cc_start: 0.9610 (ptpp) cc_final: 0.9385 (ptpp) REVERT: A 4101 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8850 (mt) REVERT: A 4108 TRP cc_start: 0.8796 (t60) cc_final: 0.8360 (t60) REVERT: B 236 ILE cc_start: 0.9016 (mm) cc_final: 0.8672 (mm) REVERT: B 251 ARG cc_start: 0.9340 (ptm160) cc_final: 0.8757 (tmm-80) REVERT: B 252 MET cc_start: 0.8962 (mmm) cc_final: 0.7199 (mmm) REVERT: B 425 ASP cc_start: 0.7924 (p0) cc_final: 0.7675 (p0) REVERT: B 444 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7755 (mt-10) REVERT: B 566 VAL cc_start: 0.9634 (p) cc_final: 0.9422 (p) REVERT: B 625 ASP cc_start: 0.9231 (t0) cc_final: 0.9014 (t0) REVERT: B 631 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8900 (tt0) REVERT: C 440 ARG cc_start: 0.9261 (tpp80) cc_final: 0.8925 (tpp80) REVERT: C 675 MET cc_start: 0.9472 (mmm) cc_final: 0.9123 (mmm) REVERT: C 693 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8550 (tm-30) REVERT: C 697 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 613 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8310 (tp-100) REVERT: D 621 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8151 (p) REVERT: D 629 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: D 675 MET cc_start: 0.9632 (ttp) cc_final: 0.9325 (ppp) outliers start: 32 outliers final: 23 residues processed: 239 average time/residue: 0.1108 time to fit residues: 42.2764 Evaluate side-chains 219 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 192 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3268 ASP Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3709 LEU Chi-restraints excluded: chain A residue 3871 LEU Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 621 THR Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 28 optimal weight: 3.9990 chunk 174 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 203 optimal weight: 0.0010 chunk 200 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 202 optimal weight: 40.0000 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A3736 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN D 636 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.081262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.059825 restraints weight = 76872.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060581 restraints weight = 52221.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.061092 restraints weight = 37040.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.061556 restraints weight = 30280.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.061864 restraints weight = 25939.840| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 16392 Z= 0.111 Angle : 0.654 12.831 22348 Z= 0.310 Chirality : 0.042 0.247 2609 Planarity : 0.003 0.033 2830 Dihedral : 4.891 58.785 2447 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.61 % Favored : 93.34 % Rotamer: Outliers : 2.84 % Allowed : 20.84 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 2132 helix: 2.05 (0.16), residues: 1109 sheet: -0.15 (0.40), residues: 194 loop : -2.72 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A4100 TYR 0.016 0.001 TYR D 684 PHE 0.031 0.001 PHE C 480 TRP 0.012 0.001 TRP B 570 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00244 (16383) covalent geometry : angle 0.65108 (22324) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.60143 ( 6) hydrogen bonds : bond 0.03252 ( 913) hydrogen bonds : angle 3.71018 ( 2664) link_NAG-ASN : bond 0.00204 ( 6) link_NAG-ASN : angle 2.33729 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8458 (pp) REVERT: A 3290 LEU cc_start: 0.9709 (mm) cc_final: 0.9312 (tp) REVERT: A 4017 LYS cc_start: 0.9588 (ptpp) cc_final: 0.9364 (ptpp) REVERT: A 4101 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 4108 TRP cc_start: 0.8806 (t60) cc_final: 0.8441 (t60) REVERT: B 236 ILE cc_start: 0.8996 (mm) cc_final: 0.8651 (mm) REVERT: B 251 ARG cc_start: 0.9354 (ptm160) cc_final: 0.8677 (tmm-80) REVERT: B 252 MET cc_start: 0.8980 (mmm) cc_final: 0.7617 (mmm) REVERT: B 425 ASP cc_start: 0.7908 (p0) cc_final: 0.7657 (p0) REVERT: B 444 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7691 (mt-10) REVERT: C 440 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8927 (tpp80) REVERT: C 631 GLU cc_start: 0.9570 (tp30) cc_final: 0.9162 (tp30) REVERT: C 675 MET cc_start: 0.9486 (mmm) cc_final: 0.9123 (mmm) REVERT: C 682 ASP cc_start: 0.8843 (p0) cc_final: 0.8417 (p0) REVERT: C 693 GLN cc_start: 0.9186 (tp-100) cc_final: 0.8868 (tm-30) REVERT: C 697 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7937 (mm-30) REVERT: D 613 GLN cc_start: 0.8913 (tp-100) cc_final: 0.8326 (tp-100) REVERT: D 629 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: D 675 MET cc_start: 0.9638 (OUTLIER) cc_final: 0.9336 (ppp) outliers start: 41 outliers final: 24 residues processed: 227 average time/residue: 0.1088 time to fit residues: 39.5019 Evaluate side-chains 222 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3268 ASP Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3709 LEU Chi-restraints excluded: chain A residue 3850 VAL Chi-restraints excluded: chain A residue 3871 LEU Chi-restraints excluded: chain A residue 4000 VAL Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 629 PHE Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 177 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 175 optimal weight: 50.0000 chunk 144 optimal weight: 5.9990 chunk 115 optimal weight: 30.0000 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 30.0000 chunk 205 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 GLN ** C 694 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.080247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.059312 restraints weight = 78494.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060375 restraints weight = 49842.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060872 restraints weight = 36263.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.061254 restraints weight = 30010.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061679 restraints weight = 26087.149| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16392 Z= 0.127 Angle : 0.660 13.261 22348 Z= 0.315 Chirality : 0.042 0.250 2609 Planarity : 0.003 0.032 2830 Dihedral : 4.714 58.517 2447 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.56 % Allowed : 21.68 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.19), residues: 2132 helix: 2.03 (0.16), residues: 1111 sheet: -0.31 (0.39), residues: 201 loop : -2.70 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4100 TYR 0.016 0.001 TYR D 684 PHE 0.028 0.001 PHE C 480 TRP 0.014 0.001 TRP B 570 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00277 (16383) covalent geometry : angle 0.65603 (22324) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.92945 ( 6) hydrogen bonds : bond 0.03323 ( 913) hydrogen bonds : angle 3.75587 ( 2664) link_NAG-ASN : bond 0.00241 ( 6) link_NAG-ASN : angle 2.58068 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8486 (pp) REVERT: A 3290 LEU cc_start: 0.9719 (mm) cc_final: 0.9313 (tp) REVERT: A 3678 MET cc_start: 0.8952 (mmm) cc_final: 0.8669 (mmm) REVERT: A 4017 LYS cc_start: 0.9596 (ptpp) cc_final: 0.9375 (ptpp) REVERT: A 4101 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8860 (mt) REVERT: A 4108 TRP cc_start: 0.8767 (t60) cc_final: 0.8404 (t60) REVERT: B 251 ARG cc_start: 0.9364 (ptm160) cc_final: 0.8692 (tmm-80) REVERT: B 252 MET cc_start: 0.8995 (mmm) cc_final: 0.7663 (mmm) REVERT: B 425 ASP cc_start: 0.7990 (p0) cc_final: 0.7738 (p0) REVERT: B 444 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7721 (mt-10) REVERT: B 625 ASP cc_start: 0.9178 (t0) cc_final: 0.8960 (t0) REVERT: B 698 MET cc_start: 0.8238 (ppp) cc_final: 0.7128 (ppp) REVERT: C 440 ARG cc_start: 0.9305 (tpp80) cc_final: 0.8964 (tpp80) REVERT: C 631 GLU cc_start: 0.9562 (tp30) cc_final: 0.9159 (tp30) REVERT: C 675 MET cc_start: 0.9481 (mmm) cc_final: 0.9102 (mmm) REVERT: C 693 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8514 (tm-30) REVERT: C 697 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 613 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8499 (tp-100) REVERT: D 675 MET cc_start: 0.9641 (OUTLIER) cc_final: 0.9347 (ppp) outliers start: 37 outliers final: 28 residues processed: 219 average time/residue: 0.1099 time to fit residues: 38.2669 Evaluate side-chains 219 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3268 ASP Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3709 LEU Chi-restraints excluded: chain A residue 3850 VAL Chi-restraints excluded: chain A residue 3871 LEU Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 666 PHE Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 182 optimal weight: 40.0000 chunk 153 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 GLN ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.080023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.059140 restraints weight = 80123.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060196 restraints weight = 49925.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.060957 restraints weight = 35892.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.061270 restraints weight = 28760.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061591 restraints weight = 25318.206| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16392 Z= 0.117 Angle : 0.674 13.395 22348 Z= 0.319 Chirality : 0.042 0.250 2609 Planarity : 0.003 0.032 2830 Dihedral : 4.543 58.716 2447 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 2.22 % Allowed : 22.51 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.19), residues: 2132 helix: 2.04 (0.16), residues: 1114 sheet: -0.33 (0.39), residues: 202 loop : -2.70 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3269 TYR 0.019 0.001 TYR D 684 PHE 0.027 0.001 PHE C 480 TRP 0.015 0.001 TRP B 570 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00258 (16383) covalent geometry : angle 0.67214 (22324) SS BOND : bond 0.00211 ( 3) SS BOND : angle 1.16594 ( 6) hydrogen bonds : bond 0.03279 ( 913) hydrogen bonds : angle 3.71817 ( 2664) link_NAG-ASN : bond 0.00222 ( 6) link_NAG-ASN : angle 1.66165 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8500 (pp) REVERT: A 3290 LEU cc_start: 0.9730 (mm) cc_final: 0.9314 (tp) REVERT: A 3678 MET cc_start: 0.8958 (mmm) cc_final: 0.8738 (mmm) REVERT: A 4017 LYS cc_start: 0.9600 (ptpp) cc_final: 0.9376 (ptpp) REVERT: A 4101 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8919 (mt) REVERT: A 4108 TRP cc_start: 0.8769 (t60) cc_final: 0.8475 (t60) REVERT: B 251 ARG cc_start: 0.9372 (ptm160) cc_final: 0.8664 (tmm-80) REVERT: B 252 MET cc_start: 0.8955 (mmm) cc_final: 0.7648 (mmm) REVERT: B 425 ASP cc_start: 0.7966 (p0) cc_final: 0.7713 (p0) REVERT: B 444 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7744 (mt-10) REVERT: B 625 ASP cc_start: 0.9186 (t0) cc_final: 0.8977 (t0) REVERT: C 440 ARG cc_start: 0.9326 (tpp80) cc_final: 0.9001 (tpp80) REVERT: C 675 MET cc_start: 0.9475 (mmm) cc_final: 0.9088 (mmm) REVERT: C 693 GLN cc_start: 0.9165 (tp-100) cc_final: 0.8487 (tm-30) REVERT: C 697 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7781 (mm-30) REVERT: D 675 MET cc_start: 0.9648 (OUTLIER) cc_final: 0.9357 (ppp) outliers start: 32 outliers final: 23 residues processed: 217 average time/residue: 0.0913 time to fit residues: 32.4049 Evaluate side-chains 221 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3709 LEU Chi-restraints excluded: chain A residue 3850 VAL Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 182 optimal weight: 50.0000 chunk 184 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 5 optimal weight: 50.0000 chunk 115 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 GLN D 613 GLN D 622 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.058211 restraints weight = 79646.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.059166 restraints weight = 49758.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.059708 restraints weight = 36386.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060152 restraints weight = 29485.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.060601 restraints weight = 25844.035| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16392 Z= 0.134 Angle : 0.690 13.713 22348 Z= 0.326 Chirality : 0.042 0.269 2609 Planarity : 0.003 0.031 2830 Dihedral : 4.512 58.766 2447 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.41 % Favored : 92.54 % Rotamer: Outliers : 2.01 % Allowed : 22.58 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.19), residues: 2132 helix: 2.06 (0.16), residues: 1118 sheet: -0.41 (0.39), residues: 207 loop : -2.62 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3269 TYR 0.021 0.001 TYR D 684 PHE 0.029 0.001 PHE C 480 TRP 0.038 0.001 TRP A3842 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00294 (16383) covalent geometry : angle 0.68875 (22324) SS BOND : bond 0.00267 ( 3) SS BOND : angle 1.02075 ( 6) hydrogen bonds : bond 0.03335 ( 913) hydrogen bonds : angle 3.73515 ( 2664) link_NAG-ASN : bond 0.00133 ( 6) link_NAG-ASN : angle 1.66705 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8537 (pp) REVERT: A 3290 LEU cc_start: 0.9744 (mm) cc_final: 0.9354 (tp) REVERT: A 3678 MET cc_start: 0.8970 (mmm) cc_final: 0.8751 (mmm) REVERT: A 4017 LYS cc_start: 0.9609 (ptpp) cc_final: 0.9382 (ptpp) REVERT: A 4019 LEU cc_start: 0.9726 (mt) cc_final: 0.9516 (mt) REVERT: A 4101 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8856 (mt) REVERT: A 4108 TRP cc_start: 0.8768 (t60) cc_final: 0.8411 (t60) REVERT: B 251 ARG cc_start: 0.9352 (ptm160) cc_final: 0.8639 (tmm-80) REVERT: B 252 MET cc_start: 0.8960 (mmm) cc_final: 0.7650 (mmm) REVERT: B 425 ASP cc_start: 0.7994 (p0) cc_final: 0.7752 (p0) REVERT: B 444 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7719 (mt-10) REVERT: B 625 ASP cc_start: 0.9218 (t0) cc_final: 0.9011 (t0) REVERT: C 440 ARG cc_start: 0.9355 (tpp80) cc_final: 0.9024 (tpp80) REVERT: C 675 MET cc_start: 0.9475 (mmm) cc_final: 0.9093 (mmm) REVERT: C 693 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8552 (tm-30) REVERT: C 697 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7939 (mm-30) REVERT: D 613 GLN cc_start: 0.9335 (tp-100) cc_final: 0.8629 (tp-100) REVERT: D 675 MET cc_start: 0.9693 (OUTLIER) cc_final: 0.9250 (ppp) outliers start: 29 outliers final: 23 residues processed: 211 average time/residue: 0.0976 time to fit residues: 33.1608 Evaluate side-chains 218 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3850 VAL Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain A residue 4104 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 38 optimal weight: 7.9990 chunk 206 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 11 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 overall best weight: 2.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 456 GLN D 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.078276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.057732 restraints weight = 82059.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.058640 restraints weight = 51708.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059150 restraints weight = 37478.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.059580 restraints weight = 30766.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059975 restraints weight = 26583.202| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16392 Z= 0.132 Angle : 0.710 14.297 22348 Z= 0.333 Chirality : 0.043 0.283 2609 Planarity : 0.003 0.031 2830 Dihedral : 4.505 58.708 2447 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 2.08 % Allowed : 22.65 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 2132 helix: 2.06 (0.16), residues: 1119 sheet: -0.41 (0.39), residues: 207 loop : -2.61 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3269 TYR 0.017 0.001 TYR D 684 PHE 0.028 0.001 PHE C 480 TRP 0.024 0.001 TRP A3795 HIS 0.005 0.001 HIS C 501 Details of bonding type rmsd covalent geometry : bond 0.00293 (16383) covalent geometry : angle 0.70872 (22324) SS BOND : bond 0.00255 ( 3) SS BOND : angle 0.55289 ( 6) hydrogen bonds : bond 0.03368 ( 913) hydrogen bonds : angle 3.74789 ( 2664) link_NAG-ASN : bond 0.00149 ( 6) link_NAG-ASN : angle 1.63044 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3253 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8537 (pp) REVERT: A 3290 LEU cc_start: 0.9750 (mm) cc_final: 0.9344 (tp) REVERT: A 3678 MET cc_start: 0.8920 (mmm) cc_final: 0.8697 (mmm) REVERT: A 4017 LYS cc_start: 0.9596 (ptpp) cc_final: 0.9351 (ptpp) REVERT: A 4019 LEU cc_start: 0.9709 (mt) cc_final: 0.9505 (mt) REVERT: A 4101 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8864 (mt) REVERT: A 4108 TRP cc_start: 0.8684 (t60) cc_final: 0.8342 (t60) REVERT: B 251 ARG cc_start: 0.9311 (ptm160) cc_final: 0.8621 (tmm-80) REVERT: B 252 MET cc_start: 0.8916 (mmm) cc_final: 0.7606 (mmm) REVERT: B 425 ASP cc_start: 0.7922 (p0) cc_final: 0.7684 (p0) REVERT: B 444 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 625 ASP cc_start: 0.9177 (t0) cc_final: 0.8976 (t0) REVERT: C 440 ARG cc_start: 0.9346 (tpp80) cc_final: 0.9012 (tpp80) REVERT: C 675 MET cc_start: 0.9405 (mmm) cc_final: 0.9109 (mmm) REVERT: C 693 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8543 (tm-30) REVERT: C 697 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7926 (mm-30) REVERT: D 675 MET cc_start: 0.9667 (OUTLIER) cc_final: 0.9240 (ppp) outliers start: 30 outliers final: 25 residues processed: 214 average time/residue: 0.1006 time to fit residues: 34.4768 Evaluate side-chains 220 residues out of total 1877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3085 LEU Chi-restraints excluded: chain A residue 3094 ILE Chi-restraints excluded: chain A residue 3253 LEU Chi-restraints excluded: chain A residue 3288 ILE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3342 PHE Chi-restraints excluded: chain A residue 3676 VAL Chi-restraints excluded: chain A residue 3850 VAL Chi-restraints excluded: chain A residue 3902 LEU Chi-restraints excluded: chain A residue 4101 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 656 LEU Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 284 GLU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 481 CYS Chi-restraints excluded: chain C residue 672 LEU Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 622 GLN Chi-restraints excluded: chain D residue 675 MET Chi-restraints excluded: chain D residue 690 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 2 optimal weight: 9.9990 chunk 169 optimal weight: 50.0000 chunk 186 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 180 optimal weight: 50.0000 chunk 63 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 179 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 430 ASN C 456 GLN D 613 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.055193 restraints weight = 79094.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.055867 restraints weight = 54552.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056389 restraints weight = 39458.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.056817 restraints weight = 32371.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.057257 restraints weight = 28384.911| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16392 Z= 0.195 Angle : 0.728 14.367 22348 Z= 0.351 Chirality : 0.043 0.288 2609 Planarity : 0.003 0.036 2830 Dihedral : 4.665 58.263 2447 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.11 % Favored : 91.84 % Rotamer: Outliers : 2.08 % Allowed : 22.58 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 2132 helix: 1.99 (0.16), residues: 1128 sheet: -0.45 (0.39), residues: 204 loop : -2.60 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3269 TYR 0.017 0.001 TYR D 684 PHE 0.027 0.001 PHE C 480 TRP 0.018 0.002 TRP A3795 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd covalent geometry : bond 0.00425 (16383) covalent geometry : angle 0.72683 (22324) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.54446 ( 6) hydrogen bonds : bond 0.03620 ( 913) hydrogen bonds : angle 3.92209 ( 2664) link_NAG-ASN : bond 0.00134 ( 6) link_NAG-ASN : angle 1.83786 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.87 seconds wall clock time: 48 minutes 11.41 seconds (2891.41 seconds total)