Starting phenix.real_space_refine on Sun Jun 15 19:45:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6h_39799/06_2025/8z6h_39799_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 82 5.16 5 C 11521 2.51 5 N 2895 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17589 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 5794 Classifications: {'peptide': 784} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 32, 'TRANS': 751} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 500 Unresolved non-hydrogen dihedrals: 335 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 233 Chain: "B" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3913 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 10, 'TRANS': 463} Chain breaks: 1 Chain: "C" Number of atoms: 3928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3928 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 10, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 3819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3819 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 10, 'TRANS': 452} Chain breaks: 1 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.01, per 1000 atoms: 0.57 Number of scatterers: 17589 At special positions: 0 Unit cell: (127.179, 158.702, 125.005, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 1 15.00 O 3090 8.00 N 2895 7.00 C 11521 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A3770 " - pdb=" SG CYS A3811 " distance=2.03 Simple disulfide: pdb=" SG CYS A4051 " - pdb=" SG CYS A4075 " distance=2.03 Simple disulfide: pdb=" SG CYS A4066 " - pdb=" SG CYS A4087 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG B1001 " - " ASN B 375 " " NAG B1002 " - " ASN B 328 " " NAG C1001 " - " ASN C 328 " " NAG C1002 " - " ASN C 375 " " NAG D1001 " - " ASN D 328 " " NAG D1002 " - " ASN D 375 " Time building additional restraints: 4.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4162 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 6 sheets defined 57.0% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3102 removed outlier: 4.125A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A3088 " --> pdb=" O CYS A3084 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A3093 " --> pdb=" O MET A3089 " (cutoff:3.500A) Processing helix chain 'A' and resid 3247 through 3252 removed outlier: 3.811A pdb=" N GLU A3252 " --> pdb=" O LEU A3248 " (cutoff:3.500A) Processing helix chain 'A' and resid 3262 through 3266 removed outlier: 3.846A pdb=" N SER A3265 " --> pdb=" O ILE A3262 " (cutoff:3.500A) removed outlier: 4.286A 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 3301 Processing helix chain 'A' and resid 3322 through 3338 removed outlier: 3.777A pdb=" N GLY A3326 " --> pdb=" O THR A3322 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A3328 " --> pdb=" O ALA A3324 " (cutoff:3.500A) Proline residue: A3335 - end of helix Processing helix chain 'A' and resid 3557 through 3578 removed outlier: 3.884A pdb=" N ALA A3578 " --> pdb=" O GLY A3574 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3602 removed outlier: 3.609A pdb=" N SER A3585 " --> pdb=" O PRO A3581 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL A3586 " --> pdb=" O PRO A3582 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA A3587 " --> pdb=" O GLY A3583 " (cutoff:3.500A) Processing helix chain 'A' and resid 3603 through 3608 removed outlier: 3.821A pdb=" N VAL A3608 " --> pdb=" O GLU A3604 " (cutoff:3.500A) Processing helix chain 'A' and resid 3656 through 3689 removed outlier: 3.640A pdb=" N GLU A3660 " --> pdb=" O LEU A3656 " (cutoff:3.500A) Processing helix chain 'A' and resid 3692 through 3709 removed outlier: 4.177A pdb=" N GLY A3696 " --> pdb=" O ALA A3692 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N HIS A3697 " --> pdb=" O SER A3693 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A3699 " --> pdb=" O HIS A3695 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A3700 " --> pdb=" O GLY A3696 " (cutoff:3.500A) Processing helix chain 'A' and resid 3710 through 3716 Processing helix chain 'A' and resid 3722 through 3730 Processing helix chain 'A' and resid 3730 through 3736 Processing helix chain 'A' and resid 3826 through 3840 Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.663A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3925 Processing helix chain 'A' and resid 3928 through 3932 removed outlier: 4.150A pdb=" N LEU A3931 " --> pdb=" O TRP A3928 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG A3932 " --> pdb=" O ARG A3929 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3928 through 3932' Processing helix chain 'A' and resid 3936 through 3968 removed outlier: 3.649A pdb=" N ARG A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4005 Processing helix chain 'A' and resid 4006 through 4009 removed outlier: 3.567A 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 4022 removed outlier: 3.695A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4047 removed outlier: 3.812A pdb=" N LEU A4047 " --> pdb=" O LEU A4043 " (cutoff:3.500A) Processing helix chain 'A' and resid 4057 through 4062 Processing helix chain 'A' and resid 4081 through 4096 removed outlier: 3.711A pdb=" N LEU A4085 " --> pdb=" O HIS A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4100 through 4114 removed outlier: 3.849A pdb=" N VAL A4104 " --> pdb=" O ARG A4100 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A4105 " --> pdb=" O LEU A4101 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TRP A4108 " --> pdb=" O VAL A4104 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 242 removed outlier: 3.636A pdb=" N GLU B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.509A pdb=" N THR B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 334 through 338 removed outlier: 3.627A pdb=" N ARG B 338 " --> pdb=" O GLN B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.758A 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 Processing helix chain 'B' and resid 467 through 497 Processing helix chain 'B' and resid 508 through 530 removed outlier: 3.535A pdb=" N SER B 530 " --> pdb=" O ILE B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.524A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 576 Processing helix chain 'B' and resid 580 through 620 removed outlier: 3.623A pdb=" N GLN B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 removed outlier: 3.531A pdb=" N LEU B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 653 removed outlier: 4.020A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN B 653 " --> pdb=" O ILE B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 671 through 697 removed outlier: 3.885A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 246 through 258 Processing helix chain 'C' and resid 269 through 273 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 removed outlier: 3.829A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 495 Processing helix chain 'C' and resid 505 through 530 removed outlier: 3.603A pdb=" N SER C 530 " --> pdb=" O ILE C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 removed outlier: 3.591A pdb=" N LEU C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 572 Processing helix chain 'C' and resid 573 through 576 Processing helix chain 'C' and resid 580 through 620 removed outlier: 3.691A pdb=" N ALA C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LYS C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASP C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 642 removed outlier: 3.659A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.542A pdb=" N ASN C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.666A pdb=" N TYR C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 698 Processing helix chain 'D' and resid 220 through 241 Processing helix chain 'D' and resid 245 through 258 removed outlier: 4.006A pdb=" N TYR D 249 " --> pdb=" O ASN D 245 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU D 256 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE D 257 " --> pdb=" O MET D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.671A pdb=" N GLY D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 291' Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.519A pdb=" N LEU D 337 " --> pdb=" O PRO D 334 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 338 " --> pdb=" O GLN D 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 334 through 338' Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 494 removed outlier: 3.830A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 484 " --> pdb=" O PHE D 480 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 485 " --> pdb=" O CYS D 481 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 486 " --> pdb=" O PHE D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 504 removed outlier: 3.615A pdb=" N ARG D 504 " --> pdb=" O HIS D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 536 removed outlier: 3.713A pdb=" N ASP D 511 " --> pdb=" O TRP D 507 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL D 512 " --> pdb=" O ASN D 508 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 529 " --> pdb=" O ASN D 525 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 530 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL D 534 " --> pdb=" O SER D 530 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 576 removed outlier: 4.148A pdb=" N ALA D 552 " --> pdb=" O PHE D 548 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TRP D 554 " --> pdb=" O HIS D 550 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 576 " --> pdb=" O LYS D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 620 removed outlier: 3.540A pdb=" N SER D 584 " --> pdb=" O ASN D 580 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 641 Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 657 through 670 Processing helix chain 'D' and resid 674 through 698 removed outlier: 3.868A pdb=" N ALA D 678 " --> pdb=" O ASN D 674 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3139 through 3141 Processing sheet with id=AA2, first strand: chain 'A' and resid 3749 through 3751 Processing sheet with id=AA3, first strand: chain 'A' and resid 3857 through 3858 removed outlier: 5.064A pdb=" N ALA A3865 " --> pdb=" O PHE A3888 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE A3888 " --> pdb=" O ALA A3865 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL A3867 " --> pdb=" O ARG A3886 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ARG A3886 " --> pdb=" O VAL A3867 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N LEU A3869 " --> pdb=" O SER A3884 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER A3884 " --> pdb=" O LEU A3869 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU A3871 " --> pdb=" O ALA A3882 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA A3882 " --> pdb=" O LEU A3871 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N PHE A3873 " --> pdb=" O LEU A3880 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU A3880 " --> pdb=" O PHE A3873 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A3875 " --> pdb=" O ARG A3878 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.607A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.542A 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: 6.553A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 391 through 394 removed outlier: 7.039A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 437 " --> pdb=" O VAL D 428 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2733 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: 5.41 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2703 1.31 - 1.43: 5350 1.43 - 1.56: 9856 1.56 - 1.69: 2 1.69 - 1.82: 123 Bond restraints: 18034 Sorted by residual: bond pdb=" C19 PGW A4401 " pdb=" O03 PGW A4401 " ideal model delta sigma weight residual 1.332 1.399 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C1 PGW A4401 " pdb=" O01 PGW A4401 " ideal model delta sigma weight residual 1.332 1.397 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O14 PGW A4401 " pdb=" P PGW A4401 " ideal model delta sigma weight residual 1.512 1.457 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O13 PGW A4401 " pdb=" P PGW A4401 " ideal model delta sigma weight residual 1.495 1.456 0.039 2.00e-02 2.50e+03 3.82e+00 bond pdb=" C02 PGW A4401 " pdb=" O01 PGW A4401 " ideal model delta sigma weight residual 1.427 1.396 0.031 2.00e-02 2.50e+03 2.42e+00 ... (remaining 18029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 24435 3.77 - 7.54: 64 7.54 - 11.30: 7 11.30 - 15.07: 0 15.07 - 18.84: 1 Bond angle restraints: 24507 Sorted by residual: angle pdb=" O13 PGW A4401 " pdb=" P PGW A4401 " pdb=" O14 PGW A4401 " ideal model delta sigma weight residual 119.81 100.97 18.84 3.00e+00 1.11e-01 3.94e+01 angle pdb=" C GLU A3853 " pdb=" N LEU A3854 " pdb=" CA LEU A3854 " ideal model delta sigma weight residual 121.90 115.46 6.44 1.26e+00 6.30e-01 2.61e+01 angle pdb=" N VAL C 532 " pdb=" CA VAL C 532 " pdb=" C VAL C 532 " ideal model delta sigma weight residual 111.91 108.28 3.63 8.90e-01 1.26e+00 1.66e+01 angle pdb=" O11 PGW A4401 " pdb=" P PGW A4401 " pdb=" O12 PGW A4401 " ideal model delta sigma weight residual 98.90 110.19 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" N SER A4050 " pdb=" CA SER A4050 " pdb=" C SER A4050 " ideal model delta sigma weight residual 112.97 109.15 3.82 1.06e+00 8.90e-01 1.30e+01 ... (remaining 24502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.05: 10308 33.05 - 66.09: 220 66.09 - 99.14: 20 99.14 - 132.19: 1 132.19 - 165.23: 4 Dihedral angle restraints: 10553 sinusoidal: 4114 harmonic: 6439 Sorted by residual: dihedral pdb=" CB CYS A3770 " pdb=" SG CYS A3770 " pdb=" SG CYS A3811 " pdb=" CB CYS A3811 " ideal model delta sinusoidal sigma weight residual 93.00 145.17 -52.17 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA PHE D 482 " pdb=" C PHE D 482 " pdb=" N PHE D 483 " pdb=" CA PHE D 483 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C11 PGW A4401 " pdb=" C12 PGW A4401 " pdb=" C13 PGW A4401 " pdb=" C14 PGW A4401 " ideal model delta sinusoidal sigma weight residual -179.90 -14.67 -165.23 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 10550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 2786 0.238 - 0.476: 3 0.476 - 0.715: 0 0.715 - 0.953: 0 0.953 - 1.191: 1 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 375 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -3.59 1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 328 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CB ILE C 495 " pdb=" CA ILE C 495 " pdb=" CG1 ILE C 495 " pdb=" CG2 ILE C 495 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 2787 not shown) Planarity restraints: 3054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1002 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG D1002 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D1002 " -0.115 2.00e-02 2.50e+03 pdb=" N2 NAG D1002 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG D1002 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1001 " -0.195 2.00e-02 2.50e+03 1.61e-01 3.24e+02 pdb=" C7 NAG D1001 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG D1001 " -0.141 2.00e-02 2.50e+03 pdb=" N2 NAG D1001 " 0.262 2.00e-02 2.50e+03 pdb=" O7 NAG D1001 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1002 " 0.167 2.00e-02 2.50e+03 1.41e-01 2.49e+02 pdb=" C7 NAG B1002 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG B1002 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B1002 " -0.227 2.00e-02 2.50e+03 pdb=" O7 NAG B1002 " 0.133 2.00e-02 2.50e+03 ... (remaining 3051 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1068 2.74 - 3.28: 17622 3.28 - 3.82: 28030 3.82 - 4.36: 31842 4.36 - 4.90: 57085 Nonbonded interactions: 135647 Sorted by model distance: nonbonded pdb=" OH TYR D 227 " pdb=" O VAL D 569 " model vdw 2.195 3.040 nonbonded pdb=" O GLY A3804 " pdb=" OG SER A3816 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU A4025 " pdb=" OH TYR D 684 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 349 " pdb=" OG SER B 352 " model vdw 2.230 3.040 nonbonded pdb=" OG SER C 349 " pdb=" OG SER C 352 " model vdw 2.266 3.040 ... (remaining 135642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 219 through 293 or resid 311 through 698 or resid 1001 thr \ ough 1002)) selection = (chain 'C' and (resid 219 through 293 or resid 311 through 698 or resid 1001 thr \ ough 1002)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 39.360 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 0.401 18045 Z= 0.204 Angle : 0.645 22.766 24535 Z= 0.307 Chirality : 0.046 1.191 2790 Planarity : 0.007 0.306 3048 Dihedral : 14.223 165.234 6376 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.90 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2174 helix: 1.63 (0.16), residues: 1152 sheet: -0.44 (0.39), residues: 199 loop : -2.32 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A3806 HIS 0.004 0.001 HIS B 498 PHE 0.017 0.001 PHE D 600 TYR 0.009 0.001 TYR C 502 ARG 0.004 0.000 ARG D 420 Details of bonding type rmsd link_NAG-ASN : bond 0.16914 ( 6) link_NAG-ASN : angle 11.24980 ( 18) hydrogen bonds : bond 0.14524 ( 941) hydrogen bonds : angle 5.07738 ( 2733) SS BOND : bond 0.00185 ( 5) SS BOND : angle 1.84848 ( 10) covalent geometry : bond 0.00262 (18034) covalent geometry : angle 0.56749 (24507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5632 (mtp180) cc_final: 0.5193 (tpt90) REVERT: A 3264 LEU cc_start: 0.8186 (tt) cc_final: 0.7977 (tt) REVERT: A 3603 TRP cc_start: 0.5940 (m-90) cc_final: 0.5697 (m100) REVERT: A 3659 GLU cc_start: 0.7296 (pp20) cc_final: 0.5945 (mm-30) REVERT: A 4090 LEU cc_start: 0.9457 (tp) cc_final: 0.9247 (tp) REVERT: B 335 GLN cc_start: 0.7833 (pm20) cc_final: 0.7477 (tp-100) REVERT: B 456 GLN cc_start: 0.8362 (tt0) cc_final: 0.8004 (tt0) REVERT: B 581 ARG cc_start: 0.7628 (mpp-170) cc_final: 0.6989 (mtm-85) REVERT: D 251 ARG cc_start: 0.7644 (tpp80) cc_final: 0.7130 (tpp80) REVERT: D 531 ASN cc_start: 0.6981 (m-40) cc_final: 0.6661 (t0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3450 time to fit residues: 112.1670 Evaluate side-chains 153 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3096 HIS A3261 HIS B 245 ASN ** B 498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN D 313 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.138576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094117 restraints weight = 26837.520| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.45 r_work: 0.2991 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18045 Z= 0.151 Angle : 0.555 12.876 24535 Z= 0.288 Chirality : 0.040 0.170 2790 Planarity : 0.004 0.036 3048 Dihedral : 8.140 132.706 2575 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.22 % Favored : 92.69 % Rotamer: Outliers : 1.10 % Allowed : 6.81 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2174 helix: 1.85 (0.16), residues: 1157 sheet: -0.48 (0.38), residues: 199 loop : -2.22 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 293 HIS 0.009 0.001 HIS A3096 PHE 0.017 0.001 PHE D 482 TYR 0.019 0.001 TYR D 247 ARG 0.005 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 6) link_NAG-ASN : angle 2.41279 ( 18) hydrogen bonds : bond 0.05350 ( 941) hydrogen bonds : angle 4.13252 ( 2733) SS BOND : bond 0.00186 ( 5) SS BOND : angle 1.67879 ( 10) covalent geometry : bond 0.00344 (18034) covalent geometry : angle 0.55038 (24507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5615 (mtp180) cc_final: 0.5026 (tpt90) REVERT: A 3264 LEU cc_start: 0.8281 (tt) cc_final: 0.7936 (tt) REVERT: A 3603 TRP cc_start: 0.6519 (m-90) cc_final: 0.6207 (m100) REVERT: A 3659 GLU cc_start: 0.7316 (pp20) cc_final: 0.6048 (mm-30) REVERT: A 3691 ASP cc_start: 0.7851 (p0) cc_final: 0.7582 (p0) REVERT: B 335 GLN cc_start: 0.7970 (pm20) cc_final: 0.7489 (tp-100) REVERT: B 456 GLN cc_start: 0.8992 (tt0) cc_final: 0.8626 (tt0) REVERT: B 581 ARG cc_start: 0.8345 (mpp-170) cc_final: 0.7731 (mtm-85) REVERT: C 650 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8436 (tm-30) REVERT: D 251 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7818 (tpp80) REVERT: D 531 ASN cc_start: 0.7266 (m-40) cc_final: 0.6480 (t0) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 0.3922 time to fit residues: 106.2701 Evaluate side-chains 172 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 153 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 179 optimal weight: 10.0000 chunk 204 optimal weight: 0.8980 chunk 169 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 198 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN D 323 GLN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.094373 restraints weight = 26846.303| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.45 r_work: 0.2993 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18045 Z= 0.129 Angle : 0.517 13.661 24535 Z= 0.270 Chirality : 0.039 0.161 2790 Planarity : 0.003 0.039 3048 Dihedral : 7.100 117.453 2575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.69 % Rotamer: Outliers : 1.32 % Allowed : 9.18 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2174 helix: 2.04 (0.16), residues: 1141 sheet: -0.45 (0.38), residues: 199 loop : -2.17 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3785 HIS 0.003 0.001 HIS C 379 PHE 0.015 0.001 PHE D 600 TYR 0.015 0.001 TYR D 527 ARG 0.005 0.000 ARG A3856 Details of bonding type rmsd link_NAG-ASN : bond 0.00097 ( 6) link_NAG-ASN : angle 1.82363 ( 18) hydrogen bonds : bond 0.04967 ( 941) hydrogen bonds : angle 3.97276 ( 2733) SS BOND : bond 0.00182 ( 5) SS BOND : angle 1.43610 ( 10) covalent geometry : bond 0.00284 (18034) covalent geometry : angle 0.51426 (24507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5670 (mtp180) cc_final: 0.5030 (tpt90) REVERT: A 3264 LEU cc_start: 0.8335 (tt) cc_final: 0.7942 (tt) REVERT: A 3603 TRP cc_start: 0.6535 (m-90) cc_final: 0.6208 (m100) REVERT: A 3659 GLU cc_start: 0.7311 (pp20) cc_final: 0.5761 (mm-30) REVERT: A 3662 ARG cc_start: 0.7796 (ttp80) cc_final: 0.7291 (ttp80) REVERT: A 3691 ASP cc_start: 0.7891 (p0) cc_final: 0.7532 (p0) REVERT: A 3808 TRP cc_start: 0.7026 (t60) cc_final: 0.6715 (t60) REVERT: B 335 GLN cc_start: 0.7978 (pm20) cc_final: 0.7493 (tp-100) REVERT: B 456 GLN cc_start: 0.9016 (tt0) cc_final: 0.8657 (tt0) REVERT: B 494 GLU cc_start: 0.8506 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 581 ARG cc_start: 0.8367 (mpp-170) cc_final: 0.7599 (mtp-110) REVERT: B 650 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8421 (tt0) REVERT: C 650 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8390 (tm-30) REVERT: D 251 ARG cc_start: 0.8554 (tpp80) cc_final: 0.7977 (tpp80) REVERT: D 531 ASN cc_start: 0.7280 (m-40) cc_final: 0.6950 (m110) outliers start: 24 outliers final: 20 residues processed: 186 average time/residue: 0.4364 time to fit residues: 127.0556 Evaluate side-chains 184 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 323 GLN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088945 restraints weight = 27078.895| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.41 r_work: 0.2912 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18045 Z= 0.258 Angle : 0.612 13.861 24535 Z= 0.322 Chirality : 0.043 0.192 2790 Planarity : 0.004 0.061 3048 Dihedral : 7.127 113.922 2575 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.82 % Favored : 92.09 % Rotamer: Outliers : 1.70 % Allowed : 11.04 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2174 helix: 1.77 (0.15), residues: 1150 sheet: -0.54 (0.38), residues: 199 loop : -2.24 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 414 HIS 0.005 0.001 HIS D 379 PHE 0.019 0.002 PHE D 482 TYR 0.016 0.002 TYR C 348 ARG 0.009 0.000 ARG D 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 6) link_NAG-ASN : angle 1.99140 ( 18) hydrogen bonds : bond 0.06346 ( 941) hydrogen bonds : angle 4.13577 ( 2733) SS BOND : bond 0.00339 ( 5) SS BOND : angle 2.38163 ( 10) covalent geometry : bond 0.00623 (18034) covalent geometry : angle 0.60801 (24507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5715 (mtp180) cc_final: 0.5123 (tpt90) REVERT: A 3264 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8056 (tt) REVERT: A 3603 TRP cc_start: 0.6785 (m-90) cc_final: 0.6075 (m100) REVERT: A 3659 GLU cc_start: 0.7340 (pp20) cc_final: 0.7077 (pp20) REVERT: A 3691 ASP cc_start: 0.7985 (p0) cc_final: 0.7622 (p0) REVERT: A 3808 TRP cc_start: 0.7248 (t60) cc_final: 0.6953 (t60) REVERT: B 335 GLN cc_start: 0.7991 (pm20) cc_final: 0.7479 (tp-100) REVERT: B 581 ARG cc_start: 0.8406 (mpp-170) cc_final: 0.7662 (mtp-110) REVERT: C 337 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8448 (mt) REVERT: C 650 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8441 (tm-30) REVERT: D 531 ASN cc_start: 0.7328 (m-40) cc_final: 0.7012 (m110) REVERT: D 648 GLU cc_start: 0.8525 (mp0) cc_final: 0.8306 (mp0) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.3228 time to fit residues: 83.6375 Evaluate side-chains 172 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 125 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 201 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN D 313 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.091818 restraints weight = 27212.395| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.45 r_work: 0.2954 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18045 Z= 0.154 Angle : 0.535 13.930 24535 Z= 0.281 Chirality : 0.040 0.160 2790 Planarity : 0.004 0.037 3048 Dihedral : 6.791 105.411 2575 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.01 % Rotamer: Outliers : 1.92 % Allowed : 12.36 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 2174 helix: 1.87 (0.15), residues: 1157 sheet: -0.41 (0.38), residues: 197 loop : -2.27 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A3785 HIS 0.004 0.001 HIS C 379 PHE 0.018 0.001 PHE D 482 TYR 0.017 0.001 TYR A3088 ARG 0.006 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 6) link_NAG-ASN : angle 1.82617 ( 18) hydrogen bonds : bond 0.05395 ( 941) hydrogen bonds : angle 3.98631 ( 2733) SS BOND : bond 0.00229 ( 5) SS BOND : angle 1.70264 ( 10) covalent geometry : bond 0.00356 (18034) covalent geometry : angle 0.53189 (24507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 2.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5773 (mtp180) cc_final: 0.5031 (tpt90) REVERT: A 3264 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7992 (tt) REVERT: A 3691 ASP cc_start: 0.7950 (p0) cc_final: 0.7624 (p0) REVERT: A 3808 TRP cc_start: 0.7149 (t60) cc_final: 0.6812 (t60) REVERT: B 335 GLN cc_start: 0.8038 (pm20) cc_final: 0.7506 (tp-100) REVERT: B 494 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 581 ARG cc_start: 0.8361 (mpp-170) cc_final: 0.7586 (mtp-110) REVERT: B 650 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8390 (tt0) REVERT: C 337 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (mt) REVERT: C 650 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8371 (tm-30) REVERT: D 531 ASN cc_start: 0.7386 (m-40) cc_final: 0.7062 (m110) outliers start: 35 outliers final: 23 residues processed: 184 average time/residue: 0.3856 time to fit residues: 109.2560 Evaluate side-chains 179 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3744 LEU Chi-restraints excluded: chain A residue 3916 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LYS Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 59 optimal weight: 0.0970 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 199 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 323 GLN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095623 restraints weight = 27012.450| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.45 r_work: 0.3023 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18045 Z= 0.101 Angle : 0.490 14.374 24535 Z= 0.256 Chirality : 0.038 0.155 2790 Planarity : 0.003 0.037 3048 Dihedral : 6.420 99.176 2575 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 1.26 % Allowed : 13.85 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2174 helix: 2.08 (0.16), residues: 1150 sheet: -0.21 (0.39), residues: 194 loop : -2.16 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 380 HIS 0.004 0.001 HIS A3789 PHE 0.021 0.001 PHE D 482 TYR 0.020 0.001 TYR A3088 ARG 0.005 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 6) link_NAG-ASN : angle 1.68053 ( 18) hydrogen bonds : bond 0.04329 ( 941) hydrogen bonds : angle 3.79718 ( 2733) SS BOND : bond 0.00345 ( 5) SS BOND : angle 1.58213 ( 10) covalent geometry : bond 0.00201 (18034) covalent geometry : angle 0.48746 (24507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5704 (mtp180) cc_final: 0.4871 (tpt90) REVERT: A 3264 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7893 (tt) REVERT: A 3603 TRP cc_start: 0.6769 (m-90) cc_final: 0.6400 (m100) REVERT: A 3691 ASP cc_start: 0.7941 (p0) cc_final: 0.7635 (p0) REVERT: B 335 GLN cc_start: 0.7989 (pm20) cc_final: 0.7506 (tp-100) REVERT: B 494 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8128 (tm-30) REVERT: B 581 ARG cc_start: 0.8274 (mpp-170) cc_final: 0.7543 (mtp-110) REVERT: B 650 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8475 (tt0) REVERT: C 650 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8403 (tm-30) REVERT: C 698 MET cc_start: 0.7453 (tpp) cc_final: 0.7199 (mmp) REVERT: D 485 PHE cc_start: 0.8096 (t80) cc_final: 0.7889 (t80) REVERT: D 531 ASN cc_start: 0.7082 (m-40) cc_final: 0.6767 (m110) outliers start: 23 outliers final: 18 residues processed: 177 average time/residue: 0.3729 time to fit residues: 101.6314 Evaluate side-chains 173 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 40 optimal weight: 0.0980 chunk 190 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN C 498 HIS ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.139017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094574 restraints weight = 26950.589| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.45 r_work: 0.3000 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18045 Z= 0.115 Angle : 0.494 14.846 24535 Z= 0.258 Chirality : 0.038 0.153 2790 Planarity : 0.003 0.036 3048 Dihedral : 6.295 97.184 2575 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 1.26 % Allowed : 14.40 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2174 helix: 2.15 (0.16), residues: 1144 sheet: -0.22 (0.38), residues: 196 loop : -2.10 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3785 HIS 0.007 0.001 HIS C 498 PHE 0.021 0.001 PHE D 482 TYR 0.021 0.001 TYR A3088 ARG 0.007 0.000 ARG A4114 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 6) link_NAG-ASN : angle 1.66838 ( 18) hydrogen bonds : bond 0.04508 ( 941) hydrogen bonds : angle 3.76894 ( 2733) SS BOND : bond 0.00178 ( 5) SS BOND : angle 1.63867 ( 10) covalent geometry : bond 0.00251 (18034) covalent geometry : angle 0.49148 (24507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5685 (mtp180) cc_final: 0.4908 (tpt90) REVERT: A 3264 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 3603 TRP cc_start: 0.6856 (m-90) cc_final: 0.6290 (m100) REVERT: A 3691 ASP cc_start: 0.7955 (p0) cc_final: 0.7639 (p0) REVERT: A 3808 TRP cc_start: 0.6991 (t60) cc_final: 0.6704 (t60) REVERT: B 335 GLN cc_start: 0.8020 (pm20) cc_final: 0.7563 (tp-100) REVERT: B 494 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 581 ARG cc_start: 0.8252 (mpp-170) cc_final: 0.7523 (mtp-110) REVERT: B 650 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8444 (tt0) REVERT: C 650 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8378 (tm-30) REVERT: C 698 MET cc_start: 0.7480 (tpp) cc_final: 0.7226 (mmp) REVERT: D 485 PHE cc_start: 0.8132 (t80) cc_final: 0.7931 (t80) REVERT: D 531 ASN cc_start: 0.7235 (m-40) cc_final: 0.6914 (m110) outliers start: 23 outliers final: 19 residues processed: 176 average time/residue: 0.3232 time to fit residues: 86.5620 Evaluate side-chains 176 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 202 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 chunk 187 optimal weight: 9.9990 chunk 180 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 89 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN D 531 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.138602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094199 restraints weight = 26935.036| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.44 r_work: 0.2992 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18045 Z= 0.123 Angle : 0.504 15.410 24535 Z= 0.262 Chirality : 0.039 0.157 2790 Planarity : 0.003 0.036 3048 Dihedral : 6.214 96.862 2575 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 1.21 % Allowed : 14.73 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2174 helix: 2.11 (0.15), residues: 1151 sheet: -0.23 (0.38), residues: 196 loop : -2.10 (0.22), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3785 HIS 0.003 0.001 HIS C 379 PHE 0.020 0.001 PHE D 482 TYR 0.024 0.001 TYR A3088 ARG 0.005 0.000 ARG A4114 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 6) link_NAG-ASN : angle 1.65053 ( 18) hydrogen bonds : bond 0.04624 ( 941) hydrogen bonds : angle 3.77721 ( 2733) SS BOND : bond 0.00198 ( 5) SS BOND : angle 1.56248 ( 10) covalent geometry : bond 0.00275 (18034) covalent geometry : angle 0.50093 (24507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5706 (mtp180) cc_final: 0.4907 (tpt90) REVERT: A 3264 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 3603 TRP cc_start: 0.6889 (m-90) cc_final: 0.6251 (m100) REVERT: A 3691 ASP cc_start: 0.7962 (p0) cc_final: 0.7641 (p0) REVERT: A 3808 TRP cc_start: 0.7005 (t60) cc_final: 0.6722 (t60) REVERT: B 335 GLN cc_start: 0.8048 (pm20) cc_final: 0.7590 (tp-100) REVERT: B 494 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8076 (tm-30) REVERT: B 581 ARG cc_start: 0.8237 (mpp-170) cc_final: 0.7528 (mtp-110) REVERT: B 650 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8474 (tt0) REVERT: C 337 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 650 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 698 MET cc_start: 0.7478 (tpp) cc_final: 0.7219 (mmp) REVERT: D 251 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8055 (ttm170) REVERT: D 531 ASN cc_start: 0.7100 (m110) cc_final: 0.6865 (m110) outliers start: 22 outliers final: 19 residues processed: 173 average time/residue: 0.4128 time to fit residues: 109.5902 Evaluate side-chains 177 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 125 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 323 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.136135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.091499 restraints weight = 27119.768| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.44 r_work: 0.2946 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18045 Z= 0.178 Angle : 0.546 15.219 24535 Z= 0.286 Chirality : 0.041 0.171 2790 Planarity : 0.004 0.045 3048 Dihedral : 6.314 97.749 2575 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.22 % Favored : 92.73 % Rotamer: Outliers : 1.54 % Allowed : 14.56 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 2174 helix: 2.01 (0.15), residues: 1153 sheet: -0.36 (0.38), residues: 199 loop : -2.13 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3806 HIS 0.004 0.001 HIS C 379 PHE 0.020 0.001 PHE D 482 TYR 0.026 0.002 TYR A3088 ARG 0.005 0.000 ARG D 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 6) link_NAG-ASN : angle 1.80227 ( 18) hydrogen bonds : bond 0.05455 ( 941) hydrogen bonds : angle 3.90136 ( 2733) SS BOND : bond 0.00265 ( 5) SS BOND : angle 1.92608 ( 10) covalent geometry : bond 0.00421 (18034) covalent geometry : angle 0.54299 (24507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5496 (mtp180) cc_final: 0.4718 (tpt90) REVERT: A 3264 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 3691 ASP cc_start: 0.7982 (p0) cc_final: 0.7657 (p0) REVERT: A 3808 TRP cc_start: 0.7094 (t60) cc_final: 0.6836 (t60) REVERT: B 335 GLN cc_start: 0.8078 (pm20) cc_final: 0.7583 (tp-100) REVERT: B 494 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 581 ARG cc_start: 0.8345 (mpp-170) cc_final: 0.7606 (mtp-110) REVERT: C 337 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8375 (mt) REVERT: C 650 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8438 (tm-30) REVERT: C 698 MET cc_start: 0.7461 (tpp) cc_final: 0.7204 (mmp) REVERT: D 251 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8130 (ttm170) REVERT: D 531 ASN cc_start: 0.6996 (m110) cc_final: 0.6696 (t0) outliers start: 28 outliers final: 23 residues processed: 174 average time/residue: 0.3256 time to fit residues: 85.1612 Evaluate side-chains 175 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 649 ILE Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 596 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.138270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.093887 restraints weight = 26823.639| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.44 r_work: 0.2986 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18045 Z= 0.118 Angle : 0.507 15.657 24535 Z= 0.264 Chirality : 0.039 0.166 2790 Planarity : 0.003 0.036 3048 Dihedral : 6.135 94.671 2575 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 1.21 % Allowed : 14.95 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2174 helix: 2.12 (0.15), residues: 1151 sheet: -0.27 (0.38), residues: 197 loop : -2.09 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3806 HIS 0.003 0.001 HIS B 379 PHE 0.020 0.001 PHE D 482 TYR 0.024 0.001 TYR A3088 ARG 0.006 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 6) link_NAG-ASN : angle 1.65007 ( 18) hydrogen bonds : bond 0.04699 ( 941) hydrogen bonds : angle 3.80570 ( 2733) SS BOND : bond 0.00208 ( 5) SS BOND : angle 1.52254 ( 10) covalent geometry : bond 0.00258 (18034) covalent geometry : angle 0.50459 (24507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4348 Ramachandran restraints generated. 2174 Oldfield, 0 Emsley, 2174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5440 (mtp180) cc_final: 0.4687 (tpt90) REVERT: A 3264 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7903 (tt) REVERT: A 3691 ASP cc_start: 0.7967 (p0) cc_final: 0.7646 (p0) REVERT: A 3808 TRP cc_start: 0.7012 (t60) cc_final: 0.6757 (t60) REVERT: B 335 GLN cc_start: 0.8061 (pm20) cc_final: 0.7571 (tp-100) REVERT: B 494 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 581 ARG cc_start: 0.8329 (mpp-170) cc_final: 0.7599 (mtp-110) REVERT: B 650 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8355 (tt0) REVERT: C 337 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8318 (mt) REVERT: C 650 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8380 (tm-30) REVERT: C 698 MET cc_start: 0.7633 (tpp) cc_final: 0.7349 (mmp) REVERT: D 251 ARG cc_start: 0.8800 (tpp80) cc_final: 0.8190 (ttm170) REVERT: D 531 ASN cc_start: 0.6975 (m110) cc_final: 0.6686 (t0) outliers start: 22 outliers final: 19 residues processed: 171 average time/residue: 0.3216 time to fit residues: 82.9197 Evaluate side-chains 175 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3065 VAL Chi-restraints excluded: chain A residue 3264 LEU Chi-restraints excluded: chain A residue 3333 VAL Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3572 VAL Chi-restraints excluded: chain A residue 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Chi-restraints excluded: chain D residue 535 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 27 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.088587 restraints weight = 27199.294| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.44 r_work: 0.2900 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 18045 Z= 0.291 Angle : 0.634 15.715 24535 Z= 0.334 Chirality : 0.044 0.182 2790 Planarity : 0.004 0.071 3048 Dihedral : 6.558 95.113 2575 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 1.59 % Allowed : 14.62 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2174 helix: 1.75 (0.15), residues: 1161 sheet: -0.47 (0.38), residues: 199 loop : -2.23 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A3806 HIS 0.005 0.001 HIS D 379 PHE 0.018 0.002 PHE C 423 TYR 0.028 0.002 TYR A3088 ARG 0.008 0.001 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 6) link_NAG-ASN : angle 2.02441 ( 18) hydrogen bonds : bond 0.06589 ( 941) hydrogen bonds : angle 4.09249 ( 2733) SS BOND : bond 0.00380 ( 5) SS BOND : angle 2.47732 ( 10) covalent geometry : bond 0.00711 (18034) covalent geometry : angle 0.63048 (24507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12275.91 seconds wall clock time: 218 minutes 26.20 seconds (13106.20 seconds total)