Starting phenix.real_space_refine on Sat Jul 4 02:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797.map" model { file = "/net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z6b_39797/07_2026/8z6b_39797_neut_trim.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 81 5.16 5 C 11489 2.51 5 N 2893 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17549 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 5757 Classifications: {'peptide': 783} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 31, 'TRANS': 751} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 358 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'ARG:plan': 10, 'PHE:plan': 6, 'TYR:plan': 2, 'GLU:plan': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'ASP:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 237 Chain: "B" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3933 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 10, 'TRANS': 465} 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {'NAG': 2, 'PA8': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.02, per 1000 atoms: 0.17 Number of scatterers: 17549 At special positions: 0 Unit cell: (126.092, 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 81 16.00 P 1 15.00 O 3085 8.00 N 2893 7.00 C 11489 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 A4075 " - 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 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 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=1, 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 D4202 " - " ASN D 328 " " NAG D4203 " - " ASN D 375 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 653.0 milliseconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4164 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 5 sheets defined 58.1% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 3074 through 3104 removed outlier: 4.306A pdb=" N MET A3078 " --> pdb=" O ASN A3074 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER A3104 " --> pdb=" O GLN A3100 " (cutoff:3.500A) Processing helix chain 'A' and resid 3249 through 3254 Processing helix chain 'A' and resid 3261 through 3266 removed outlier: 4.411A pdb=" N ILE A3266 " --> pdb=" O TRP A3263 " (cutoff:3.500A) Processing helix chain 'A' and resid 3278 through 3302 removed outlier: 3.531A pdb=" N VAL A3302 " --> pdb=" O TRP A3298 " (cutoff:3.500A) Processing helix chain 'A' and resid 3321 through 3345 removed outlier: 4.025A 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: 3.971A pdb=" N ALA A3578 " --> pdb=" O GLY A3574 " (cutoff:3.500A) Processing helix chain 'A' and resid 3581 through 3602 Processing helix chain 'A' and resid 3603 through 3608 Processing helix chain 'A' and resid 3656 through 3689 removed outlier: 3.887A pdb=" N ALA A3661 " --> pdb=" O ALA A3657 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG A3662 " --> pdb=" O LYS A3658 " (cutoff:3.500A) Processing helix chain 'A' and resid 3693 through 3708 removed outlier: 3.778A pdb=" N HIS A3697 " --> pdb=" O SER A3693 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A3699 " --> pdb=" O HIS A3695 " (cutoff:3.500A) removed outlier: 3.655A 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 3731 through 3736 Processing helix chain 'A' and resid 3826 through 3840 removed outlier: 3.541A pdb=" N ASP A3832 " --> pdb=" O GLU A3828 " (cutoff:3.500A) Processing helix chain 'A' and resid 3892 through 3896 removed outlier: 3.584A pdb=" N GLY A3896 " --> pdb=" O LEU A3893 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3924 Processing helix chain 'A' and resid 3932 through 3935 removed outlier: 3.682A pdb=" N ALA A3935 " --> pdb=" O ARG A3932 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3932 through 3935' Processing helix chain 'A' and resid 3936 through 3969 removed outlier: 3.731A pdb=" N LEU A3940 " --> pdb=" O TRP A3936 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A3941 " --> pdb=" O ALA A3937 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A3968 " --> pdb=" O THR A3964 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY A3969 " --> pdb=" O ARG A3965 " (cutoff:3.500A) Processing helix chain 'A' and resid 3977 through 4005 Processing helix chain 'A' and resid 4006 through 4009 removed outlier: 3.622A 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: 3.891A pdb=" N LYS A4017 " --> pdb=" O SER A4013 " (cutoff:3.500A) Processing helix chain 'A' and resid 4022 through 4049 removed outlier: 3.563A pdb=" N LEU A4026 " --> pdb=" O ALA A4022 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A4049 " --> pdb=" O ILE A4045 " (cutoff:3.500A) Processing helix chain 'A' and resid 4056 through 4063 Processing helix chain 'A' and resid 4071 through 4075 Processing helix chain 'A' and resid 4076 through 4081 Processing helix chain 'A' and resid 4083 through 4095 removed outlier: 3.848A pdb=" N CYS A4087 " --> pdb=" O SER A4083 " (cutoff:3.500A) Processing helix chain 'A' and resid 4097 through 4099 No H-bonds generated for 'chain 'A' and resid 4097 through 4099' Processing helix chain 'A' and resid 4100 through 4118 removed outlier: 3.799A pdb=" N VAL A4104 " --> pdb=" O ARG A4100 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A4105 " --> pdb=" O LEU A4101 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP A4108 " --> pdb=" O VAL A4104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY A4115 " --> pdb=" O HIS A4111 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A4117 " --> pdb=" O LEU A4113 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR A4118 " --> pdb=" O ARG A4114 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.557A pdb=" N ARG B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.620A 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 Processing helix chain 'B' and resid 363 through 367 removed outlier: 3.856A pdb=" N ILE B 367 " --> pdb=" O THR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 498 removed outlier: 3.583A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 530 Processing helix chain 'B' and resid 532 through 540 removed outlier: 3.598A pdb=" N LEU B 536 " --> pdb=" O VAL B 532 " (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: 3.526A pdb=" N LEU B 586 " --> pdb=" O THR B 582 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LYS B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET B 603 " --> pdb=" O GLY B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 642 Processing helix chain 'B' and resid 645 through 652 removed outlier: 4.389A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 671 through 697 removed outlier: 3.707A pdb=" N PHE B 676 " --> pdb=" O LEU B 672 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 240 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 removed outlier: 3.528A pdb=" N TYR C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.913A pdb=" N GLU C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 367 removed outlier: 3.689A pdb=" N TRP C 366 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 367 " --> pdb=" O THR C 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 363 through 367' Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 495 removed outlier: 3.509A pdb=" N PHE C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 530 removed outlier: 3.555A pdb=" N ASP C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 541 Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 576 Processing helix chain 'C' and resid 580 through 593 Processing helix chain 'C' and resid 593 through 620 removed outlier: 3.868A pdb=" N MET C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 641 removed outlier: 3.655A pdb=" N ILE C 640 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU C 641 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.533A pdb=" N GLU C 651 " --> pdb=" O ALA C 647 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.698A pdb=" N TYR C 660 " --> pdb=" O LEU C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 696 Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.900A pdb=" N THR D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 258 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 292 removed outlier: 3.521A pdb=" N TYR D 292 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 338 removed outlier: 3.737A pdb=" N ARG D 338 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 367 removed outlier: 3.749A pdb=" N TRP D 366 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D 367 " --> pdb=" O THR D 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 363 through 367' Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 496 removed outlier: 3.660A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 529 removed outlier: 3.613A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 536 Processing helix chain 'D' and resid 549 through 576 removed outlier: 3.825A pdb=" N ALA D 563 " --> pdb=" O ASN D 559 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL D 564 " --> pdb=" O ASN D 560 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE D 574 " --> pdb=" O TRP D 570 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS D 575 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 620 removed outlier: 5.167A pdb=" N LYS D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 5.292A 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 656 through 670 removed outlier: 3.770A pdb=" N TYR D 660 " --> pdb=" O LEU D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 673 No H-bonds generated for 'chain 'D' and resid 671 through 673' Processing helix chain 'D' and resid 674 through 697 removed outlier: 3.759A pdb=" N ALA D 678 " --> pdb=" O ASN D 674 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3138 through 3142 Processing sheet with id=AA2, first strand: chain 'A' and resid 3819 through 3821 removed outlier: 3.731A pdb=" N ARG A3748 " --> pdb=" O GLU A3853 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A3853 " --> pdb=" O ARG A3748 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.598A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.562A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.659A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) 980 hydrogen bonds defined for protein. 2832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.04 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 - 1.44: 5352 1.44 - 1.56: 9814 1.56 - 1.69: 2 1.69 - 1.82: 122 Bond restraints: 17993 Sorted by residual: bond pdb=" C12 PA8 D4201 " pdb=" O7 PA8 D4201 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C4 PA8 D4201 " pdb=" O5 PA8 D4201 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG D4203 " pdb=" O5 NAG D4203 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O4 PA8 D4201 " pdb=" P1 PA8 D4201 " ideal model delta sigma weight residual 1.707 1.648 0.059 2.00e-02 2.50e+03 8.79e+00 bond pdb=" C2 PA8 D4201 " pdb=" O7 PA8 D4201 " ideal model delta sigma weight residual 1.438 1.398 0.040 2.00e-02 2.50e+03 3.98e+00 ... (remaining 17988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 24034 1.75 - 3.50: 337 3.50 - 5.25: 67 5.25 - 7.00: 13 7.00 - 8.75: 6 Bond angle restraints: 24457 Sorted by residual: angle pdb=" C VAL C 623 " pdb=" N ASP C 624 " pdb=" CA ASP C 624 " ideal model delta sigma weight residual 121.54 128.32 -6.78 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C5 PA8 D4201 " pdb=" C4 PA8 D4201 " pdb=" O5 PA8 D4201 " ideal model delta sigma weight residual 111.20 119.93 -8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" C ASN D 645 " pdb=" N PHE D 646 " pdb=" CA PHE D 646 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.26e+00 angle pdb=" O3 PA8 D4201 " pdb=" P1 PA8 D4201 " pdb=" O4 PA8 D4201 " ideal model delta sigma weight residual 100.81 109.41 -8.60 3.00e+00 1.11e-01 8.22e+00 angle pdb=" C13 PA8 D4201 " pdb=" C12 PA8 D4201 " pdb=" O7 PA8 D4201 " ideal model delta sigma weight residual 111.38 119.97 -8.59 3.00e+00 1.11e-01 8.20e+00 ... (remaining 24452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.78: 9984 24.78 - 49.57: 472 49.57 - 74.35: 36 74.35 - 99.14: 11 99.14 - 123.92: 1 Dihedral angle restraints: 10504 sinusoidal: 4061 harmonic: 6443 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 -86.00 -128.00 42.00 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS A4075 " pdb=" SG CYS A4075 " pdb=" SG CYS A4087 " pdb=" CB CYS A4087 " ideal model delta sinusoidal sigma weight residual 93.00 134.55 -41.55 1 1.00e+01 1.00e-02 2.42e+01 dihedral pdb=" C2 NAG D4203 " pdb=" C1 NAG D4203 " pdb=" O5 NAG D4203 " pdb=" C5 NAG D4203 " ideal model delta sinusoidal sigma weight residual -62.96 60.96 -123.92 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 10501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2341 0.054 - 0.107: 396 0.107 - 0.161: 43 0.161 - 0.215: 1 0.215 - 0.269: 1 Chirality restraints: 2782 Sorted by residual: 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 2.38 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG D4203 " pdb=" ND2 ASN D 375 " pdb=" C2 NAG D4203 " pdb=" O5 NAG D4203 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" CA ILE D 433 " pdb=" N ILE D 433 " pdb=" C ILE D 433 " pdb=" CB ILE D 433 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 2779 not shown) Planarity restraints: 3052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A4075 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A4076 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A4076 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A4076 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 657 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 658 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 658 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 658 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A3764 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A3765 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO A3765 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A3765 " 0.019 5.00e-02 4.00e+02 ... (remaining 3049 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3109 2.77 - 3.30: 16573 3.30 - 3.83: 27965 3.83 - 4.37: 31319 4.37 - 4.90: 56564 Nonbonded interactions: 135530 Sorted by model distance: nonbonded pdb=" O LEU A3843 " pdb=" OG SER A3847 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR C 227 " pdb=" O VAL C 569 " model vdw 2.280 3.040 nonbonded pdb=" OG SER A3777 " pdb=" OH TYR A3781 " model vdw 2.292 3.040 nonbonded pdb=" OE1 GLU B 312 " pdb=" ND2 ASN B 432 " model vdw 2.298 3.120 nonbonded pdb=" NH2 ARG A3748 " pdb=" OE2 GLU A3853 " model vdw 2.301 3.120 ... (remaining 135525 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 1002)) selection = (chain 'C' and (resid 219 through 293 or resid 311 through 698 or resid 1002)) selection = (chain 'D' and (resid 219 through 698 or resid 4202)) } 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 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 : 0.006 0.703 18005 Z= 0.542 Angle : 0.559 8.753 24485 Z= 0.290 Chirality : 0.039 0.269 2782 Planarity : 0.003 0.043 3046 Dihedral : 13.753 123.920 6325 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 0.06 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 2175 helix: 1.75 (0.16), residues: 1162 sheet: -0.48 (0.39), residues: 207 loop : -2.34 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A3929 TYR 0.019 0.001 TYR A3334 PHE 0.014 0.001 PHE D 600 TRP 0.011 0.001 TRP A3724 HIS 0.003 0.000 HIS D 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (17993) covalent geometry : angle 0.55598 / 0.29 (24457) SS BOND : bond 0.00243 / 0.12 ( 5) SS BOND : angle 1.56407 / 1.36 ( 10) hydrogen bonds : bond 0.14456 / 10.14 ( 980) hydrogen bonds : angle 5.02884 / 3.75 ( 2832) Misc. bond : bond 0.70264 / 36.98 ( 1) link_NAG-ASN : bond 0.00377 / 0.13 ( 6) link_NAG-ASN : angle 1.99104 / 1.26 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.686 Fit side-chains REVERT: A 4001 LYS cc_start: 0.8509 (tptt) cc_final: 0.8258 (tppp) REVERT: B 528 ARG cc_start: 0.6886 (ttp80) cc_final: 0.6663 (ttp80) REVERT: C 251 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.8169 (ttt-90) REVERT: C 625 ASP cc_start: 0.7829 (m-30) cc_final: 0.7530 (m-30) REVERT: D 471 PHE cc_start: 0.8450 (m-80) cc_final: 0.8125 (m-80) REVERT: D 472 PHE cc_start: 0.8125 (t80) cc_final: 0.7895 (t80) outliers start: 1 outliers final: 0 residues processed: 236 average time/residue: 0.5191 time to fit residues: 139.1093 Evaluate side-chains 161 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 580 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.091653 restraints weight = 27054.253| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.57 r_work: 0.3047 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18005 Z= 0.142 Angle : 0.559 9.803 24485 Z= 0.291 Chirality : 0.040 0.237 2782 Planarity : 0.004 0.038 3046 Dihedral : 7.104 113.013 2545 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.41 % Favored : 91.49 % Rotamer: Outliers : 1.55 % Allowed : 8.14 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.19), residues: 2175 helix: 1.76 (0.15), residues: 1205 sheet: -0.57 (0.38), residues: 205 loop : -2.30 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3277 TYR 0.015 0.001 TYR C 527 PHE 0.021 0.001 PHE D 669 TRP 0.008 0.001 TRP B 554 HIS 0.005 0.001 HIS A3840 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (17993) covalent geometry : angle 0.55470 / 0.29 (24457) SS BOND : bond 0.00350 / 0.17 ( 5) SS BOND : angle 1.67662 / 1.41 ( 10) hydrogen bonds : bond 0.05097 / 3.70 ( 980) hydrogen bonds : angle 4.07120 / 3.02 ( 2832) Misc. bond : bond 0.00410 / 0.22 ( 1) link_NAG-ASN : bond 0.00374 / 0.14 ( 6) link_NAG-ASN : angle 2.43716 / 1.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.579 Fit side-chains REVERT: A 3260 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7772 (mmtp) REVERT: A 3924 ARG cc_start: 0.6397 (mmp80) cc_final: 0.6192 (mmp80) REVERT: A 4114 ARG cc_start: 0.8699 (ttt90) cc_final: 0.8280 (ttt-90) REVERT: B 266 GLU cc_start: 0.8545 (mp0) cc_final: 0.8073 (mp0) REVERT: B 528 ARG cc_start: 0.6851 (ttp80) cc_final: 0.6638 (ttp80) REVERT: B 644 ILE cc_start: 0.8783 (tp) cc_final: 0.8462 (tp) REVERT: C 251 ARG cc_start: 0.8812 (ttt-90) cc_final: 0.8557 (ttt-90) REVERT: C 416 ASP cc_start: 0.8680 (m-30) cc_final: 0.8410 (m-30) REVERT: C 490 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 491 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 528 ARG cc_start: 0.7139 (tmm-80) cc_final: 0.6566 (ttp80) REVERT: C 625 ASP cc_start: 0.8439 (m-30) cc_final: 0.8134 (m-30) REVERT: C 668 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8413 (mmt) REVERT: D 471 PHE cc_start: 0.8499 (m-80) cc_final: 0.8058 (m-80) REVERT: D 472 PHE cc_start: 0.8112 (t80) cc_final: 0.7887 (t80) REVERT: D 477 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.5374 (tm-30) REVERT: D 648 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8043 (mm-30) outliers start: 28 outliers final: 11 residues processed: 202 average time/residue: 0.5169 time to fit residues: 118.9439 Evaluate side-chains 180 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3260 LYS Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain A residue 4045 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 686 GLU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 668 MET Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 85 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4004 GLN D 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.135499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092250 restraints weight = 27464.657| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.58 r_work: 0.3058 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18005 Z= 0.126 Angle : 0.527 9.011 24485 Z= 0.274 Chirality : 0.040 0.235 2782 Planarity : 0.003 0.038 3046 Dihedral : 6.833 113.032 2545 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.86 % Favored : 92.05 % Rotamer: Outliers : 2.10 % Allowed : 10.63 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 2175 helix: 1.86 (0.15), residues: 1205 sheet: -0.44 (0.39), residues: 199 loop : -2.46 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A3280 TYR 0.022 0.001 TYR D 486 PHE 0.032 0.001 PHE D 669 TRP 0.008 0.001 TRP B 380 HIS 0.004 0.001 HIS A3840 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (17993) covalent geometry : angle 0.52263 / 0.27 (24457) SS BOND : bond 0.00321 / 0.16 ( 5) SS BOND : angle 1.48367 / 1.19 ( 10) hydrogen bonds : bond 0.04713 / 3.42 ( 980) hydrogen bonds : angle 3.90363 / 2.90 ( 2832) Misc. bond : bond 0.00319 / 0.17 ( 1) link_NAG-ASN : bond 0.00338 / 0.12 ( 6) link_NAG-ASN : angle 2.29045 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.690 Fit side-chains REVERT: A 3658 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6351 (pptt) REVERT: A 3924 ARG cc_start: 0.6374 (mmp80) cc_final: 0.6115 (mmp80) REVERT: A 4001 LYS cc_start: 0.8497 (tppp) cc_final: 0.8227 (ttmm) REVERT: A 4114 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8269 (ttt-90) REVERT: B 266 GLU cc_start: 0.8484 (mp0) cc_final: 0.7814 (mp0) REVERT: B 643 ASP cc_start: 0.8508 (t0) cc_final: 0.8171 (t0) REVERT: C 251 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8591 (ttt-90) REVERT: C 416 ASP cc_start: 0.8633 (m-30) cc_final: 0.8336 (m-30) REVERT: C 528 ARG cc_start: 0.7030 (tmm-80) cc_final: 0.6540 (ttp80) REVERT: D 471 PHE cc_start: 0.8502 (m-80) cc_final: 0.8069 (m-80) REVERT: D 472 PHE cc_start: 0.7937 (t80) cc_final: 0.7610 (t80) REVERT: D 486 TYR cc_start: 0.8018 (t80) cc_final: 0.7804 (t80) outliers start: 38 outliers final: 12 residues processed: 201 average time/residue: 0.5532 time to fit residues: 125.9722 Evaluate side-chains 173 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3658 LYS Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 172 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 25 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 184 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 681 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.095263 restraints weight = 27143.042| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.73 r_work: 0.3070 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18005 Z= 0.098 Angle : 0.499 8.862 24485 Z= 0.257 Chirality : 0.038 0.216 2782 Planarity : 0.003 0.037 3046 Dihedral : 6.547 111.085 2545 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 1.22 % Allowed : 13.45 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.19), residues: 2175 helix: 2.02 (0.15), residues: 1196 sheet: -0.45 (0.39), residues: 204 loop : -2.38 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A3280 TYR 0.017 0.001 TYR D 486 PHE 0.021 0.001 PHE D 576 TRP 0.010 0.001 TRP B 380 HIS 0.004 0.000 HIS A3840 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.10 (17993) covalent geometry : angle 0.49569 / 0.26 (24457) SS BOND : bond 0.00477 / 0.29 ( 5) SS BOND : angle 1.43539 / 1.22 ( 10) hydrogen bonds : bond 0.03866 / 2.81 ( 980) hydrogen bonds : angle 3.69199 / 2.73 ( 2832) Misc. bond : bond 0.00002 / 0.00 ( 1) link_NAG-ASN : bond 0.00375 / 0.15 ( 6) link_NAG-ASN : angle 2.07771 / 1.45 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 3658 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6073 (pptt) REVERT: A 3924 ARG cc_start: 0.6198 (mmp80) cc_final: 0.5948 (mmp80) REVERT: A 3950 LEU cc_start: 0.8629 (mm) cc_final: 0.8391 (mp) REVERT: B 266 GLU cc_start: 0.8358 (mp0) cc_final: 0.7787 (mp0) REVERT: B 624 ASP cc_start: 0.6455 (m-30) cc_final: 0.6247 (m-30) REVERT: B 643 ASP cc_start: 0.8352 (t0) cc_final: 0.8017 (t0) REVERT: C 242 MET cc_start: 0.8811 (tpp) cc_final: 0.8484 (tpp) REVERT: C 416 ASP cc_start: 0.8696 (m-30) cc_final: 0.8349 (m-30) REVERT: C 528 ARG cc_start: 0.6860 (tmm-80) cc_final: 0.6357 (ttp80) REVERT: D 434 ASN cc_start: 0.7989 (t0) cc_final: 0.7763 (t0) REVERT: D 472 PHE cc_start: 0.7776 (t80) cc_final: 0.7417 (t80) outliers start: 22 outliers final: 11 residues processed: 190 average time/residue: 0.5028 time to fit residues: 109.1770 Evaluate side-chains 170 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3334 TYR Chi-restraints excluded: chain A residue 3658 LYS Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 215 optimal weight: 1.9990 chunk 13 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 50.0000 chunk 163 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS D 681 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.090210 restraints weight = 27146.902| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.59 r_work: 0.3023 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18005 Z= 0.157 Angle : 0.554 9.276 24485 Z= 0.288 Chirality : 0.040 0.251 2782 Planarity : 0.003 0.036 3046 Dihedral : 6.577 109.656 2545 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.14 % Favored : 91.77 % Rotamer: Outliers : 2.10 % Allowed : 13.84 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 2175 helix: 1.89 (0.15), residues: 1212 sheet: -0.58 (0.38), residues: 204 loop : -2.47 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.019 0.001 TYR D 486 PHE 0.018 0.001 PHE D 600 TRP 0.007 0.001 TRP B 554 HIS 0.008 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17993) covalent geometry : angle 0.54875 / 0.29 (24457) SS BOND : bond 0.00326 / 0.16 ( 5) SS BOND : angle 2.37749 / 1.78 ( 10) hydrogen bonds : bond 0.05081 / 3.69 ( 980) hydrogen bonds : angle 3.87134 / 2.88 ( 2832) Misc. bond : bond 0.00000 / 0.00 ( 1) link_NAG-ASN : bond 0.00298 / 0.11 ( 6) link_NAG-ASN : angle 2.35612 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.636 Fit side-chains REVERT: A 3843 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (tm) REVERT: A 3924 ARG cc_start: 0.6329 (mmp80) cc_final: 0.6076 (mmp80) REVERT: B 266 GLU cc_start: 0.8363 (mp0) cc_final: 0.7776 (mp0) REVERT: B 643 ASP cc_start: 0.8535 (t0) cc_final: 0.8195 (t0) REVERT: C 242 MET cc_start: 0.8778 (tpp) cc_final: 0.8442 (tpp) REVERT: C 416 ASP cc_start: 0.8660 (m-30) cc_final: 0.8383 (m-30) REVERT: C 528 ARG cc_start: 0.7017 (tmm-80) cc_final: 0.6493 (ttp80) REVERT: D 222 ARG cc_start: 0.8130 (ttp80) cc_final: 0.7793 (tmt170) REVERT: D 471 PHE cc_start: 0.8528 (m-80) cc_final: 0.8085 (m-80) REVERT: D 472 PHE cc_start: 0.7925 (t80) cc_final: 0.7557 (t80) REVERT: D 675 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7856 (mmt) outliers start: 38 outliers final: 21 residues processed: 186 average time/residue: 0.4831 time to fit residues: 103.2638 Evaluate side-chains 180 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3066 PHE Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3843 LEU Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3853 GLU Chi-restraints excluded: chain A residue 3933 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Chi-restraints excluded: chain D residue 675 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 18 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 681 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089553 restraints weight = 27177.727| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.58 r_work: 0.3010 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18005 Z= 0.169 Angle : 0.566 9.476 24485 Z= 0.295 Chirality : 0.041 0.258 2782 Planarity : 0.003 0.036 3046 Dihedral : 6.614 109.454 2545 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.46 % Favored : 91.45 % Rotamer: Outliers : 2.16 % Allowed : 14.78 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.19), residues: 2175 helix: 1.90 (0.15), residues: 1204 sheet: -0.51 (0.38), residues: 200 loop : -2.54 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A3848 TYR 0.018 0.001 TYR C 527 PHE 0.019 0.001 PHE D 600 TRP 0.007 0.001 TRP B 554 HIS 0.006 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (17993) covalent geometry : angle 0.56119 / 0.29 (24457) SS BOND : bond 0.00319 / 0.16 ( 5) SS BOND : angle 1.91368 / 1.56 ( 10) hydrogen bonds : bond 0.05188 / 3.78 ( 980) hydrogen bonds : angle 3.89811 / 2.90 ( 2832) Misc. bond : bond 0.00049 / 0.03 ( 1) link_NAG-ASN : bond 0.00312 / 0.11 ( 6) link_NAG-ASN : angle 2.38340 / 1.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.774 Fit side-chains REVERT: A 3691 ASP cc_start: 0.7995 (p0) cc_final: 0.7773 (p0) REVERT: A 3924 ARG cc_start: 0.6395 (mmp80) cc_final: 0.5961 (mmp80) REVERT: A 4001 LYS cc_start: 0.8488 (tppp) cc_final: 0.8177 (ttmm) REVERT: B 266 GLU cc_start: 0.8375 (mp0) cc_final: 0.7724 (mp0) REVERT: B 643 ASP cc_start: 0.8523 (t0) cc_final: 0.8169 (t0) REVERT: B 644 ILE cc_start: 0.8811 (tp) cc_final: 0.8488 (tp) REVERT: C 242 MET cc_start: 0.8785 (tpp) cc_final: 0.8509 (tpp) REVERT: C 416 ASP cc_start: 0.8628 (m-30) cc_final: 0.8331 (m-30) REVERT: C 528 ARG cc_start: 0.7162 (tmm-80) cc_final: 0.6647 (ttp80) REVERT: D 222 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7880 (tmt170) REVERT: D 471 PHE cc_start: 0.8517 (m-80) cc_final: 0.8074 (m-80) REVERT: D 472 PHE cc_start: 0.7963 (t80) cc_final: 0.7580 (t80) REVERT: D 477 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5423 (tm-30) REVERT: D 675 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7836 (mmt) outliers start: 39 outliers final: 22 residues processed: 190 average time/residue: 0.5233 time to fit residues: 113.0077 Evaluate side-chains 183 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3853 GLU Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain A residue 3933 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 253 MET Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 492 ILE Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Chi-restraints excluded: chain D residue 675 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 150 optimal weight: 0.9980 chunk 172 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 199 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 202 optimal weight: 0.0270 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 HIS ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.093483 restraints weight = 27090.690| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.73 r_work: 0.3044 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18005 Z= 0.103 Angle : 0.520 11.496 24485 Z= 0.267 Chirality : 0.039 0.231 2782 Planarity : 0.003 0.035 3046 Dihedral : 6.341 107.707 2545 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.54 % Favored : 92.37 % Rotamer: Outliers : 1.72 % Allowed : 15.83 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 2175 helix: 2.10 (0.15), residues: 1193 sheet: -0.47 (0.39), residues: 204 loop : -2.37 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.021 0.001 TYR D 486 PHE 0.017 0.001 PHE D 600 TRP 0.010 0.001 TRP B 380 HIS 0.006 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (17993) covalent geometry : angle 0.51581 / 0.27 (24457) SS BOND : bond 0.00309 / 0.15 ( 5) SS BOND : angle 1.63812 / 1.16 ( 10) hydrogen bonds : bond 0.03989 / 2.91 ( 980) hydrogen bonds : angle 3.68068 / 2.73 ( 2832) Misc. bond : bond 0.00030 / 0.02 ( 1) link_NAG-ASN : bond 0.00370 / 0.14 ( 6) link_NAG-ASN : angle 2.08950 / 1.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 0.614 Fit side-chains REVERT: A 3691 ASP cc_start: 0.7965 (p0) cc_final: 0.7754 (p0) REVERT: A 3924 ARG cc_start: 0.6217 (mmp80) cc_final: 0.5724 (mmp80) REVERT: A 3950 LEU cc_start: 0.8660 (mm) cc_final: 0.8408 (mp) REVERT: A 4114 ARG cc_start: 0.8628 (ttt90) cc_final: 0.8032 (ttt-90) REVERT: B 266 GLU cc_start: 0.8381 (mp0) cc_final: 0.7716 (mp0) REVERT: B 401 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: B 624 ASP cc_start: 0.6532 (m-30) cc_final: 0.6326 (m-30) REVERT: B 643 ASP cc_start: 0.8416 (t0) cc_final: 0.8128 (t0) REVERT: C 242 MET cc_start: 0.8823 (tpp) cc_final: 0.8431 (tpp) REVERT: C 416 ASP cc_start: 0.8678 (m-30) cc_final: 0.8292 (m-30) REVERT: C 528 ARG cc_start: 0.6947 (tmm-80) cc_final: 0.6452 (ttp80) REVERT: C 681 ASN cc_start: 0.8282 (m-40) cc_final: 0.7955 (m-40) REVERT: D 222 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7678 (tmt170) REVERT: D 380 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.7548 (t-100) REVERT: D 471 PHE cc_start: 0.8505 (m-80) cc_final: 0.8093 (m-80) REVERT: D 472 PHE cc_start: 0.7788 (t80) cc_final: 0.7406 (t80) REVERT: D 477 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.5136 (tm-30) outliers start: 31 outliers final: 13 residues processed: 194 average time/residue: 0.5103 time to fit residues: 113.1426 Evaluate side-chains 180 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3102 ASP Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3853 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 380 TRP Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 128 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 157 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 50.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090553 restraints weight = 27221.147| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.59 r_work: 0.3033 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.003 0.035 18005 Z= 0.150 Angle : 0.561 12.396 24485 Z= 0.290 Chirality : 0.040 0.249 2782 Planarity : 0.003 0.035 3046 Dihedral : 6.455 107.459 2545 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.37 % Favored : 91.54 % Rotamer: Outliers : 1.66 % Allowed : 16.33 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 2175 helix: 2.03 (0.15), residues: 1194 sheet: -0.54 (0.38), residues: 204 loop : -2.42 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 528 TYR 0.020 0.001 TYR C 527 PHE 0.019 0.001 PHE D 600 TRP 0.006 0.001 TRP B 554 HIS 0.007 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (17993) covalent geometry : angle 0.55717 / 0.29 (24457) SS BOND : bond 0.00294 / 0.14 ( 5) SS BOND : angle 1.76335 / 1.36 ( 10) hydrogen bonds : bond 0.04843 / 3.53 ( 980) hydrogen bonds : angle 3.81455 / 2.84 ( 2832) Misc. bond : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : bond 0.00287 / 0.10 ( 6) link_NAG-ASN : angle 2.29048 / 1.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.756 Fit side-chains REVERT: A 3691 ASP cc_start: 0.8028 (p0) cc_final: 0.7803 (p0) REVERT: A 3924 ARG cc_start: 0.6381 (mmp80) cc_final: 0.5876 (mmp80) REVERT: B 266 GLU cc_start: 0.8402 (mp0) cc_final: 0.7811 (mp0) REVERT: B 401 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8226 (mm-30) REVERT: B 643 ASP cc_start: 0.8484 (t0) cc_final: 0.8176 (t0) REVERT: C 242 MET cc_start: 0.8726 (tpp) cc_final: 0.8461 (tpp) REVERT: C 416 ASP cc_start: 0.8645 (m-30) cc_final: 0.8362 (m-30) REVERT: C 528 ARG cc_start: 0.7115 (tmm-80) cc_final: 0.6607 (ttp80) REVERT: C 583 MET cc_start: 0.9005 (mmm) cc_final: 0.8748 (mmp) REVERT: D 471 PHE cc_start: 0.8616 (m-80) cc_final: 0.8172 (m-80) REVERT: D 472 PHE cc_start: 0.7941 (t80) cc_final: 0.7540 (t80) outliers start: 30 outliers final: 16 residues processed: 186 average time/residue: 0.4876 time to fit residues: 104.0808 Evaluate side-chains 180 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3102 ASP Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3853 GLU Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 167 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093395 restraints weight = 27080.583| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.72 r_work: 0.3040 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18005 Z= 0.107 Angle : 0.527 12.333 24485 Z= 0.270 Chirality : 0.039 0.233 2782 Planarity : 0.003 0.035 3046 Dihedral : 6.249 105.570 2545 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.31 % Favored : 92.60 % Rotamer: Outliers : 1.60 % Allowed : 16.38 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 2175 helix: 2.12 (0.15), residues: 1194 sheet: -0.41 (0.39), residues: 204 loop : -2.38 (0.21), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.020 0.001 TYR D 486 PHE 0.018 0.001 PHE D 600 TRP 0.009 0.001 TRP B 380 HIS 0.010 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (17993) covalent geometry : angle 0.52333 / 0.27 (24457) SS BOND : bond 0.00218 / 0.11 ( 5) SS BOND : angle 1.44281 / 1.09 ( 10) hydrogen bonds : bond 0.04062 / 2.96 ( 980) hydrogen bonds : angle 3.68254 / 2.73 ( 2832) Misc. bond : bond 0.00022 / 0.01 ( 1) link_NAG-ASN : bond 0.00329 / 0.12 ( 6) link_NAG-ASN : angle 2.06349 / 1.48 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.580 Fit side-chains REVERT: A 3658 LYS cc_start: 0.6623 (OUTLIER) cc_final: 0.6156 (pptt) REVERT: A 3691 ASP cc_start: 0.7968 (p0) cc_final: 0.7761 (p0) REVERT: A 3924 ARG cc_start: 0.6267 (mmp80) cc_final: 0.5790 (mmp80) REVERT: A 3950 LEU cc_start: 0.8659 (mm) cc_final: 0.8408 (mp) REVERT: A 4114 ARG cc_start: 0.8633 (ttt90) cc_final: 0.8041 (ttt-90) REVERT: B 266 GLU cc_start: 0.8375 (mp0) cc_final: 0.7683 (mp0) REVERT: B 643 ASP cc_start: 0.8353 (t0) cc_final: 0.8099 (t0) REVERT: C 242 MET cc_start: 0.8802 (tpp) cc_final: 0.8451 (tpp) REVERT: C 416 ASP cc_start: 0.8690 (m-30) cc_final: 0.8329 (m-30) REVERT: C 528 ARG cc_start: 0.6962 (tmm-80) cc_final: 0.6459 (ttp80) REVERT: D 471 PHE cc_start: 0.8635 (m-80) cc_final: 0.8227 (m-80) REVERT: D 472 PHE cc_start: 0.7789 (t80) cc_final: 0.7384 (t80) outliers start: 29 outliers final: 16 residues processed: 184 average time/residue: 0.4742 time to fit residues: 100.1982 Evaluate side-chains 183 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3658 LYS Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3853 GLU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain D residue 241 MET Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 164 optimal weight: 0.0020 chunk 15 optimal weight: 8.9990 overall best weight: 2.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.088011 restraints weight = 27209.710| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.57 r_work: 0.2982 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18005 Z= 0.217 Angle : 0.624 11.815 24485 Z= 0.323 Chirality : 0.043 0.269 2782 Planarity : 0.004 0.036 3046 Dihedral : 6.582 107.690 2545 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.01 % Favored : 90.90 % Rotamer: Outliers : 1.05 % Allowed : 16.99 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.19), residues: 2175 helix: 1.89 (0.15), residues: 1203 sheet: -0.47 (0.38), residues: 201 loop : -2.56 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 528 TYR 0.021 0.002 TYR A3088 PHE 0.020 0.002 PHE D 600 TRP 0.008 0.001 TRP A3806 HIS 0.014 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (17993) covalent geometry : angle 0.61872 / 0.32 (24457) SS BOND : bond 0.00363 / 0.18 ( 5) SS BOND : angle 2.09240 / 1.65 ( 10) hydrogen bonds : bond 0.05708 / 4.16 ( 980) hydrogen bonds : angle 3.97258 / 2.96 ( 2832) Misc. bond : bond 0.00024 / 0.01 ( 1) link_NAG-ASN : bond 0.00337 / 0.14 ( 6) link_NAG-ASN : angle 2.49788 / 1.72 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.654 Fit side-chains REVERT: A 3691 ASP cc_start: 0.8034 (p0) cc_final: 0.7810 (p0) REVERT: A 3924 ARG cc_start: 0.6466 (mmp80) cc_final: 0.5994 (mmp80) REVERT: A 4001 LYS cc_start: 0.8534 (tppp) cc_final: 0.8222 (ttmm) REVERT: B 266 GLU cc_start: 0.8398 (mp0) cc_final: 0.7629 (mp0) REVERT: B 643 ASP cc_start: 0.8532 (t0) cc_final: 0.8230 (t0) REVERT: B 644 ILE cc_start: 0.8766 (tp) cc_final: 0.8450 (tp) REVERT: C 416 ASP cc_start: 0.8659 (m-30) cc_final: 0.8378 (m-30) REVERT: C 528 ARG cc_start: 0.7189 (tmm-80) cc_final: 0.6702 (ttp80) REVERT: D 343 GLU cc_start: 0.7986 (mp0) cc_final: 0.7591 (mp0) REVERT: D 471 PHE cc_start: 0.8639 (m-80) cc_final: 0.8229 (m-80) REVERT: D 472 PHE cc_start: 0.8075 (t80) cc_final: 0.7701 (t80) outliers start: 19 outliers final: 14 residues processed: 176 average time/residue: 0.4935 time to fit residues: 99.2374 Evaluate side-chains 174 residues out of total 1915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3276 THR Chi-restraints excluded: chain A residue 3568 VAL Chi-restraints excluded: chain A residue 3845 ASN Chi-restraints excluded: chain A residue 3912 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 526 ILE Chi-restraints excluded: chain D residue 550 HIS Chi-restraints excluded: chain D residue 574 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 158 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 214 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 681 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.136584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094303 restraints weight = 27343.266| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.48 r_work: 0.3089 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 18005 Z= 0.114 Angle : 0.550 12.602 24485 Z= 0.281 Chirality : 0.039 0.239 2782 Planarity : 0.003 0.036 3046 Dihedral : 6.232 106.164 2545 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.45 % Favored : 92.46 % Rotamer: Outliers : 1.00 % Allowed : 17.21 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 2175 helix: 2.09 (0.15), residues: 1191 sheet: -0.31 (0.39), residues: 199 loop : -2.43 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 528 TYR 0.019 0.001 TYR D 486 PHE 0.018 0.001 PHE D 600 TRP 0.009 0.001 TRP B 380 HIS 0.011 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17993) covalent geometry : angle 0.54615 / 0.28 (24457) SS BOND : bond 0.00225 / 0.11 ( 5) SS BOND : angle 1.50942 / 1.15 ( 10) hydrogen bonds : bond 0.04216 / 3.07 ( 980) hydrogen bonds : angle 3.74388 / 2.78 ( 2832) Misc. bond : bond 0.00036 / 0.02 ( 1) link_NAG-ASN : bond 0.00330 / 0.12 ( 6) link_NAG-ASN : angle 2.08698 / 1.48 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4936.06 seconds wall clock time: 84 minutes 53.75 seconds (5093.75 seconds total)