Starting phenix.real_space_refine on Mon May 19 00:29:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6h_39799/05_2025/8z6h_39799_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6h_39799/05_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_39799/05_2025/8z6h_39799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6h_39799/05_2025/8z6h_39799.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6h_39799/05_2025/8z6h_39799_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6h_39799/05_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-5687/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: 11.00, per 1000 atoms: 0.63 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: 4.49 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: 1.57 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: 5.22 Time building geometry restraints manager: 5.26 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 40.490 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- 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 : 1.884 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: 0.3307 time to fit residues: 106.5993 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 : 1.848 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.138607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.094132 restraints weight = 26838.324| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.46 r_work: 0.2989 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5618 (mtp180) cc_final: 0.5029 (tpt90) REVERT: A 3264 LEU cc_start: 0.8287 (tt) cc_final: 0.7943 (tt) REVERT: A 3603 TRP cc_start: 0.6518 (m-90) cc_final: 0.6206 (m100) REVERT: A 3659 GLU cc_start: 0.7313 (pp20) cc_final: 0.6045 (mm-30) REVERT: A 3691 ASP cc_start: 0.7852 (p0) cc_final: 0.7585 (p0) REVERT: B 335 GLN cc_start: 0.7968 (pm20) cc_final: 0.7488 (tp-100) REVERT: B 456 GLN cc_start: 0.8992 (tt0) cc_final: 0.8627 (tt0) REVERT: B 581 ARG cc_start: 0.8355 (mpp-170) cc_final: 0.7742 (mtm-85) REVERT: C 650 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8430 (tm-30) REVERT: D 251 ARG cc_start: 0.8457 (tpp80) cc_final: 0.7833 (tpp80) REVERT: D 531 ASN cc_start: 0.7275 (m-40) cc_final: 0.6491 (t0) outliers start: 20 outliers final: 15 residues processed: 179 average time/residue: 0.3269 time to fit residues: 87.7604 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 : 1.945 ------------------------------------------------------------------------------- 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: 10.0000 chunk 179 optimal weight: 9.9990 chunk 204 optimal weight: 0.9980 chunk 169 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.138180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093632 restraints weight = 26849.590| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.44 r_work: 0.2980 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1300 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= 0.141 Angle : 0.526 13.533 24535 Z= 0.275 Chirality : 0.040 0.165 2790 Planarity : 0.004 0.040 3048 Dihedral : 7.123 117.922 2575 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.45 % Favored : 92.50 % Rotamer: Outliers : 1.43 % Allowed : 9.40 % Favored : 89.18 % 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: 0.38 (0.19), residues: 2174 helix: 1.97 (0.16), residues: 1147 sheet: -0.48 (0.38), residues: 199 loop : -2.17 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3785 HIS 0.004 0.001 HIS C 379 PHE 0.016 0.001 PHE D 600 TYR 0.014 0.001 TYR D 527 ARG 0.007 0.000 ARG A3856 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 6) link_NAG-ASN : angle 1.83700 ( 18) hydrogen bonds : bond 0.05158 ( 941) hydrogen bonds : angle 3.99723 ( 2733) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.52825 ( 10) covalent geometry : bond 0.00319 (18034) covalent geometry : angle 0.52331 (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 199 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5612 (mtp180) cc_final: 0.4948 (tpt90) REVERT: A 3264 LEU cc_start: 0.8349 (tt) cc_final: 0.7951 (tt) REVERT: A 3603 TRP cc_start: 0.6562 (m-90) cc_final: 0.6217 (m100) REVERT: A 3659 GLU cc_start: 0.7320 (pp20) cc_final: 0.5768 (mm-30) REVERT: A 3662 ARG cc_start: 0.7767 (ttp80) cc_final: 0.7257 (ttp80) REVERT: A 3691 ASP cc_start: 0.7895 (p0) cc_final: 0.7532 (p0) REVERT: A 3808 TRP cc_start: 0.7024 (t60) cc_final: 0.6702 (t60) REVERT: B 335 GLN cc_start: 0.7976 (pm20) cc_final: 0.7481 (tp-100) REVERT: B 456 GLN cc_start: 0.8982 (tt0) cc_final: 0.8611 (tt0) REVERT: B 494 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7685 (tm-30) REVERT: B 581 ARG cc_start: 0.8312 (mpp-170) cc_final: 0.7586 (mtp-110) REVERT: B 650 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8454 (tt0) REVERT: C 650 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8402 (tm-30) REVERT: D 251 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8083 (tpp80) REVERT: D 531 ASN cc_start: 0.7284 (m-40) cc_final: 0.6949 (m110) outliers start: 26 outliers final: 21 residues processed: 188 average time/residue: 0.3238 time to fit residues: 91.5478 Evaluate side-chains 183 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 3916 VAL 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: 7.9990 chunk 141 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 14 optimal weight: 40.0000 chunk 181 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 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 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 = 0.3708 r_free = 0.3708 target = 0.132855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.087946 restraints weight = 27078.857| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.43 r_work: 0.2892 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18045 Z= 0.293 Angle : 0.658 13.992 24535 Z= 0.346 Chirality : 0.045 0.199 2790 Planarity : 0.005 0.070 3048 Dihedral : 7.280 116.091 2575 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 2.03 % Allowed : 11.48 % Favored : 86.48 % 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: 0.04 (0.19), residues: 2174 helix: 1.64 (0.15), residues: 1150 sheet: -0.58 (0.38), residues: 199 loop : -2.28 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 414 HIS 0.007 0.001 HIS D 379 PHE 0.022 0.002 PHE D 480 TYR 0.016 0.002 TYR A3088 ARG 0.010 0.001 ARG D 420 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 6) link_NAG-ASN : angle 2.06567 ( 18) hydrogen bonds : bond 0.06924 ( 941) hydrogen bonds : angle 4.24246 ( 2733) SS BOND : bond 0.00680 ( 5) SS BOND : angle 2.72132 ( 10) covalent geometry : bond 0.00708 (18034) covalent geometry : angle 0.65383 (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 190 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5749 (mtp180) cc_final: 0.5157 (tpt90) REVERT: A 3264 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8081 (tt) REVERT: A 3275 PHE cc_start: 0.6023 (OUTLIER) cc_final: 0.5349 (m-80) REVERT: A 3659 GLU cc_start: 0.7245 (pp20) cc_final: 0.7003 (pp20) REVERT: A 3691 ASP cc_start: 0.7981 (p0) cc_final: 0.7631 (p0) REVERT: A 3808 TRP cc_start: 0.7177 (t60) cc_final: 0.6843 (t60) REVERT: A 3939 TRP cc_start: 0.8415 (m100) cc_final: 0.7744 (m100) REVERT: B 335 GLN cc_start: 0.8006 (pm20) cc_final: 0.7446 (tp-100) REVERT: B 581 ARG cc_start: 0.8402 (mpp-170) cc_final: 0.7638 (mtp-110) REVERT: C 337 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8454 (mt) REVERT: C 650 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8434 (tm-30) REVERT: D 531 ASN cc_start: 0.7355 (m-40) cc_final: 0.7063 (m110) REVERT: D 648 GLU cc_start: 0.8528 (mp0) cc_final: 0.8325 (mp0) outliers start: 37 outliers final: 20 residues processed: 178 average time/residue: 0.3101 time to fit residues: 82.8205 Evaluate side-chains 170 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 3275 PHE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 125 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 6 optimal weight: 0.0170 chunk 2 optimal weight: 0.9990 chunk 176 optimal weight: 0.0870 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.138531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.094086 restraints weight = 27156.226| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.46 r_work: 0.2997 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18045 Z= 0.111 Angle : 0.505 13.680 24535 Z= 0.264 Chirality : 0.038 0.157 2790 Planarity : 0.003 0.035 3048 Dihedral : 6.639 104.300 2575 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.08 % Favored : 92.87 % Rotamer: Outliers : 1.37 % Allowed : 12.91 % 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: 0.40 (0.19), residues: 2174 helix: 1.99 (0.16), residues: 1149 sheet: -0.35 (0.38), residues: 195 loop : -2.21 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 380 HIS 0.003 0.001 HIS A3840 PHE 0.018 0.001 PHE D 482 TYR 0.016 0.001 TYR A3088 ARG 0.007 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 6) link_NAG-ASN : angle 1.75102 ( 18) hydrogen bonds : bond 0.04762 ( 941) hydrogen bonds : angle 3.90991 ( 2733) SS BOND : bond 0.00210 ( 5) SS BOND : angle 1.40479 ( 10) covalent geometry : bond 0.00227 (18034) covalent geometry : angle 0.50258 (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 183 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5727 (mtp180) cc_final: 0.5008 (tpt90) REVERT: A 3264 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7942 (tt) REVERT: A 3603 TRP cc_start: 0.6893 (m-90) cc_final: 0.6411 (m100) REVERT: A 3691 ASP cc_start: 0.7945 (p0) cc_final: 0.7596 (p0) REVERT: B 335 GLN cc_start: 0.8014 (pm20) cc_final: 0.7514 (tp-100) REVERT: B 494 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 581 ARG cc_start: 0.8351 (mpp-170) cc_final: 0.7573 (mtp-110) REVERT: B 650 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8395 (tt0) REVERT: C 337 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8319 (mt) REVERT: C 650 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8406 (tm-30) REVERT: C 698 MET cc_start: 0.7431 (tpp) cc_final: 0.7166 (mmp) REVERT: D 531 ASN cc_start: 0.7233 (m-40) cc_final: 0.6927 (m110) outliers start: 25 outliers final: 15 residues processed: 176 average time/residue: 0.3011 time to fit residues: 81.0874 Evaluate side-chains 167 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 649 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 59 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 199 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 313 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.093727 restraints weight = 27021.417| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.45 r_work: 0.2984 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18045 Z= 0.119 Angle : 0.506 14.994 24535 Z= 0.264 Chirality : 0.039 0.155 2790 Planarity : 0.003 0.038 3048 Dihedral : 6.461 102.135 2575 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.92 % Rotamer: Outliers : 1.37 % Allowed : 13.90 % Favored : 84.73 % 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: 0.48 (0.19), residues: 2174 helix: 2.05 (0.16), residues: 1150 sheet: -0.26 (0.38), residues: 194 loop : -2.17 (0.22), residues: 830 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 0.019 0.001 TYR A3088 ARG 0.005 0.000 ARG A3972 Details of bonding type rmsd link_NAG-ASN : bond 0.00063 ( 6) link_NAG-ASN : angle 1.72725 ( 18) hydrogen bonds : bond 0.04729 ( 941) hydrogen bonds : angle 3.83891 ( 2733) SS BOND : bond 0.00165 ( 5) SS BOND : angle 1.75011 ( 10) covalent geometry : bond 0.00262 (18034) covalent geometry : angle 0.50325 (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 187 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5745 (mtp180) cc_final: 0.4946 (tpt90) REVERT: A 3264 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7970 (tt) REVERT: A 3691 ASP cc_start: 0.7961 (p0) cc_final: 0.7638 (p0) REVERT: A 3808 TRP cc_start: 0.7092 (t60) cc_final: 0.6841 (t60) REVERT: B 335 GLN cc_start: 0.8017 (pm20) cc_final: 0.7537 (tp-100) REVERT: B 494 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8156 (tm-30) REVERT: B 581 ARG cc_start: 0.8300 (mpp-170) cc_final: 0.7546 (mtp-110) REVERT: B 650 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8468 (tt0) REVERT: C 337 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (mt) REVERT: C 650 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8385 (tm-30) REVERT: C 698 MET cc_start: 0.7514 (tpp) cc_final: 0.7259 (mmp) REVERT: D 485 PHE cc_start: 0.8101 (t80) cc_final: 0.7870 (t80) REVERT: D 531 ASN cc_start: 0.7227 (m-40) cc_final: 0.6909 (m110) outliers start: 25 outliers final: 19 residues processed: 178 average time/residue: 0.3189 time to fit residues: 84.9887 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 : 1.859 ------------------------------------------------------------------------------- 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 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 341 ILE 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 332 SER Chi-restraints excluded: chain C residue 337 LEU 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 314 LEU Chi-restraints excluded: chain D residue 501 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 40 optimal weight: 0.5980 chunk 190 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 180 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 82 optimal weight: 0.0370 chunk 70 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 B 434 ASN C 498 HIS 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 = 0.3810 r_free = 0.3810 target = 0.141469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097484 restraints weight = 26960.740| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.45 r_work: 0.3046 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18045 Z= 0.095 Angle : 0.485 15.000 24535 Z= 0.250 Chirality : 0.038 0.154 2790 Planarity : 0.003 0.036 3048 Dihedral : 6.162 93.237 2575 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.58 % Favored : 93.38 % Rotamer: Outliers : 1.15 % Allowed : 14.78 % 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: 0.65 (0.19), residues: 2174 helix: 2.18 (0.16), residues: 1148 sheet: -0.06 (0.39), residues: 194 loop : -2.10 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 380 HIS 0.008 0.001 HIS C 498 PHE 0.020 0.001 PHE D 482 TYR 0.021 0.001 TYR A3088 ARG 0.008 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 6) link_NAG-ASN : angle 1.56757 ( 18) hydrogen bonds : bond 0.03915 ( 941) hydrogen bonds : angle 3.70162 ( 2733) SS BOND : bond 0.00182 ( 5) SS BOND : angle 1.43891 ( 10) covalent geometry : bond 0.00181 (18034) covalent geometry : angle 0.48267 (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 193 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5700 (mtp180) cc_final: 0.4901 (tpt90) REVERT: A 3264 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7892 (tt) REVERT: A 3603 TRP cc_start: 0.6844 (m-90) cc_final: 0.6357 (m100) REVERT: A 3665 LYS cc_start: 0.8203 (ttpp) cc_final: 0.7677 (mttt) REVERT: A 3691 ASP cc_start: 0.7935 (p0) cc_final: 0.7628 (p0) REVERT: A 3808 TRP cc_start: 0.7110 (t60) cc_final: 0.6817 (t60) REVERT: B 335 GLN cc_start: 0.8038 (pm20) cc_final: 0.7589 (tp-100) REVERT: B 494 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 581 ARG cc_start: 0.8213 (mpp-170) cc_final: 0.7495 (mtp-110) REVERT: B 650 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8476 (tt0) REVERT: C 650 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 698 MET cc_start: 0.7480 (tpp) cc_final: 0.7225 (mmp) REVERT: D 251 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8127 (ttm170) REVERT: D 485 PHE cc_start: 0.8097 (t80) cc_final: 0.7876 (t80) REVERT: D 531 ASN cc_start: 0.7201 (m-40) cc_final: 0.6876 (m110) outliers start: 21 outliers final: 14 residues processed: 184 average time/residue: 0.2915 time to fit residues: 82.2266 Evaluate side-chains 173 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 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 425 ASP 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 253 MET Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 501 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 202 optimal weight: 8.9990 chunk 209 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 128 optimal weight: 0.0170 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 434 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 = 0.3789 r_free = 0.3789 target = 0.139624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.095250 restraints weight = 26966.818| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.46 r_work: 0.3012 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18045 Z= 0.114 Angle : 0.495 14.797 24535 Z= 0.256 Chirality : 0.038 0.153 2790 Planarity : 0.003 0.036 3048 Dihedral : 6.092 93.226 2575 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 1.32 % Allowed : 14.89 % 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: 0.68 (0.19), residues: 2174 helix: 2.18 (0.16), residues: 1152 sheet: -0.06 (0.39), residues: 194 loop : -2.07 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A3785 HIS 0.003 0.001 HIS C 379 PHE 0.020 0.001 PHE D 482 TYR 0.021 0.001 TYR A3088 ARG 0.006 0.000 ARG A4114 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 6) link_NAG-ASN : angle 1.60792 ( 18) hydrogen bonds : bond 0.04326 ( 941) hydrogen bonds : angle 3.69778 ( 2733) SS BOND : bond 0.00152 ( 5) SS BOND : angle 1.47520 ( 10) covalent geometry : bond 0.00251 (18034) covalent geometry : angle 0.49236 (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 183 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5738 (mtp180) cc_final: 0.4862 (tpt90) REVERT: A 3264 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7908 (tt) REVERT: A 3603 TRP cc_start: 0.6912 (m-90) cc_final: 0.6167 (m100) REVERT: A 3663 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7833 (ptmt) REVERT: A 3691 ASP cc_start: 0.7921 (p0) cc_final: 0.7596 (p0) REVERT: A 3808 TRP cc_start: 0.7052 (t60) cc_final: 0.6794 (t60) REVERT: B 335 GLN cc_start: 0.8039 (pm20) cc_final: 0.7595 (tp-100) REVERT: B 494 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8061 (tm-30) REVERT: B 581 ARG cc_start: 0.8223 (mpp-170) cc_final: 0.7519 (mtp-110) REVERT: B 650 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8477 (tt0) REVERT: C 650 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8454 (tm-30) REVERT: C 698 MET cc_start: 0.7583 (tpp) cc_final: 0.7283 (mmp) REVERT: D 251 ARG cc_start: 0.8809 (tpp80) cc_final: 0.8163 (ttm170) REVERT: D 485 PHE cc_start: 0.8106 (t80) cc_final: 0.7879 (t80) REVERT: D 531 ASN cc_start: 0.7251 (m-40) cc_final: 0.6924 (m110) outliers start: 24 outliers final: 20 residues processed: 175 average time/residue: 0.3135 time to fit residues: 82.6777 Evaluate side-chains 179 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.897 ------------------------------------------------------------------------------- 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 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 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 253 MET 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 640 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 125 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.136985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.092342 restraints weight = 27161.225| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.45 r_work: 0.2963 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1850 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= 0.160 Angle : 0.539 15.542 24535 Z= 0.280 Chirality : 0.040 0.156 2790 Planarity : 0.004 0.037 3048 Dihedral : 6.204 99.758 2575 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.69 % Rotamer: Outliers : 1.59 % Allowed : 14.78 % Favored : 83.63 % 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: 0.57 (0.19), residues: 2174 helix: 2.09 (0.15), residues: 1152 sheet: -0.29 (0.38), residues: 199 loop : -2.08 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.006 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 6) link_NAG-ASN : angle 1.74431 ( 18) hydrogen bonds : bond 0.05160 ( 941) hydrogen bonds : angle 3.83598 ( 2733) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.84605 ( 10) covalent geometry : bond 0.00375 (18034) covalent geometry : angle 0.53575 (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 183 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5459 (mtp180) cc_final: 0.4700 (tpt90) REVERT: A 3264 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7951 (tt) REVERT: A 3663 LYS cc_start: 0.8164 (ptmm) cc_final: 0.7895 (ptmt) REVERT: A 3691 ASP cc_start: 0.7971 (p0) cc_final: 0.7647 (p0) REVERT: A 3808 TRP cc_start: 0.7129 (t60) cc_final: 0.6831 (t60) REVERT: B 335 GLN cc_start: 0.8102 (pm20) cc_final: 0.7632 (tp-100) REVERT: B 494 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 581 ARG cc_start: 0.8316 (mpp-170) cc_final: 0.7582 (mtp-110) REVERT: C 337 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8353 (mt) REVERT: C 650 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8429 (tm-30) REVERT: C 698 MET cc_start: 0.7692 (tpp) cc_final: 0.7400 (mmp) REVERT: D 251 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8178 (ttm170) REVERT: D 485 PHE cc_start: 0.8116 (t80) cc_final: 0.7907 (t80) REVERT: D 531 ASN cc_start: 0.7342 (m-40) cc_final: 0.7008 (m110) outliers start: 29 outliers final: 26 residues processed: 173 average time/residue: 0.3173 time to fit residues: 82.9041 Evaluate side-chains 179 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 3854 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 341 ILE 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 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 649 ILE Chi-restraints excluded: chain D residue 253 MET 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 Chi-restraints excluded: chain D residue 640 ILE Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 202 optimal weight: 0.0060 chunk 134 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.139716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095435 restraints weight = 26852.616| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.45 r_work: 0.3014 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18045 Z= 0.101 Angle : 0.494 15.682 24535 Z= 0.255 Chirality : 0.038 0.171 2790 Planarity : 0.003 0.036 3048 Dihedral : 5.986 93.939 2575 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.67 % Favored : 93.28 % Rotamer: Outliers : 1.37 % Allowed : 14.73 % 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: 0.68 (0.19), residues: 2174 helix: 2.20 (0.15), residues: 1151 sheet: -0.11 (0.39), residues: 192 loop : -2.08 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A3806 HIS 0.003 0.001 HIS A3840 PHE 0.012 0.001 PHE D 600 TYR 0.023 0.001 TYR A3088 ARG 0.005 0.000 ARG A3662 Details of bonding type rmsd link_NAG-ASN : bond 0.00138 ( 6) link_NAG-ASN : angle 1.58534 ( 18) hydrogen bonds : bond 0.04297 ( 941) hydrogen bonds : angle 3.71739 ( 2733) SS BOND : bond 0.00135 ( 5) SS BOND : angle 1.33936 ( 10) covalent geometry : bond 0.00208 (18034) covalent geometry : angle 0.49164 (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 182 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3255 ARG cc_start: 0.5662 (mtp180) cc_final: 0.4848 (tpt90) REVERT: A 3264 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7909 (tt) REVERT: A 3603 TRP cc_start: 0.6975 (m-90) cc_final: 0.6224 (m100) REVERT: A 3691 ASP cc_start: 0.7938 (p0) cc_final: 0.7617 (p0) REVERT: A 3808 TRP cc_start: 0.7022 (t60) cc_final: 0.6734 (t60) REVERT: B 335 GLN cc_start: 0.8048 (pm20) cc_final: 0.7600 (tp-100) REVERT: B 494 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 502 TYR cc_start: 0.7638 (t80) cc_final: 0.7423 (t80) REVERT: B 581 ARG cc_start: 0.8275 (mpp-170) cc_final: 0.7562 (mtp-110) REVERT: B 650 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8482 (tt0) REVERT: C 650 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8400 (tm-30) REVERT: C 698 MET cc_start: 0.7597 (tpp) cc_final: 0.7333 (mmp) REVERT: D 251 ARG cc_start: 0.8816 (tpp80) cc_final: 0.8193 (ttm170) REVERT: D 531 ASN cc_start: 0.7284 (m-40) cc_final: 0.6936 (m110) outliers start: 25 outliers final: 22 residues processed: 173 average time/residue: 0.3047 time to fit residues: 79.6699 Evaluate side-chains 178 residues out of total 1914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 3584 VAL Chi-restraints excluded: chain A residue 3723 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3854 LEU Chi-restraints excluded: chain A residue 4048 VAL Chi-restraints excluded: chain A residue 4052 VAL Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 596 ASP Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain D residue 253 MET 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 640 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 27 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 6 optimal weight: 50.0000 chunk 184 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 50.0000 chunk 11 optimal weight: 40.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 ASN B 434 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 = 0.3751 r_free = 0.3751 target = 0.136556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.091816 restraints weight = 27125.847| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.44 r_work: 0.2953 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1921 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= 0.181 Angle : 0.547 15.761 24535 Z= 0.285 Chirality : 0.041 0.181 2790 Planarity : 0.004 0.043 3048 Dihedral : 6.111 96.938 2575 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 1.48 % Allowed : 14.67 % 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: 0.54 (0.19), residues: 2174 helix: 2.07 (0.15), residues: 1153 sheet: -0.33 (0.38), residues: 199 loop : -2.09 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A3806 HIS 0.004 0.001 HIS C 379 PHE 0.016 0.001 PHE D 600 TYR 0.023 0.002 TYR A3088 ARG 0.005 0.000 ARG A4114 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 6) link_NAG-ASN : angle 1.75972 ( 18) hydrogen bonds : bond 0.05317 ( 941) hydrogen bonds : angle 3.84426 ( 2733) SS BOND : bond 0.00264 ( 5) SS BOND : angle 1.90650 ( 10) covalent geometry : bond 0.00430 (18034) covalent geometry : angle 0.54423 (24507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10146.12 seconds wall clock time: 175 minutes 18.71 seconds (10518.71 seconds total)