Starting phenix.real_space_refine on Thu Mar 5 23:25:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432.map" model { file = "/net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7stl_25432/03_2026/7stl_25432_trim.cif" } resolution = 2.95 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= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 56 5.16 5 C 8586 2.51 5 N 2094 2.21 5 O 2356 1.98 5 H 12568 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25668 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 800, 12675 Classifications: {'peptide': 800} Link IDs: {'PTRANS': 25, 'TRANS': 774} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 159 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Restraints were copied for chains: B Time building chain proxies: 16.88, per 1000 atoms: 0.66 Number of scatterers: 25668 At special positions: 0 Unit cell: (132.84, 78.84, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 8 15.00 O 2356 8.00 N 2094 7.00 C 8586 6.00 H 12568 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 640.7 milliseconds 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3016 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 60.9% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.504A pdb=" N GLU A 150 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.525A pdb=" N GLY A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.679A pdb=" N TYR A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 352 through 355 removed outlier: 3.652A pdb=" N LYS A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 439 through 451 removed outlier: 3.877A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 451 " --> pdb=" O TRP A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.548A pdb=" N VAL A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 removed outlier: 3.878A pdb=" N ASP A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 532 removed outlier: 4.793A pdb=" N LYS A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Proline residue: A 526 - end of helix Processing helix chain 'A' and resid 545 through 550 removed outlier: 3.586A pdb=" N LEU A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 545 through 550' Processing helix chain 'A' and resid 557 through 569 removed outlier: 4.054A pdb=" N GLY A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU A 566 " --> pdb=" O TYR A 562 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE A 567 " --> pdb=" O PHE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 599 through 602 Processing helix chain 'A' and resid 603 through 613 removed outlier: 4.221A pdb=" N LEU A 607 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 609 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 661 removed outlier: 4.094A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 647 " --> pdb=" O GLN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.560A pdb=" N VAL A 665 " --> pdb=" O PHE A 662 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 667 " --> pdb=" O LYS A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 694 removed outlier: 3.503A pdb=" N PHE A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.577A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 745 Processing helix chain 'A' and resid 750 through 787 removed outlier: 3.938A pdb=" N TYR A 754 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 798 Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.940A pdb=" N ALA A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 831 removed outlier: 3.523A pdb=" N SER A 831 " --> pdb=" O HIS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 853 Proline residue: A 840 - end of helix removed outlier: 3.501A pdb=" N VAL A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 846 " --> pdb=" O TYR A 842 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN A 847 " --> pdb=" O VAL A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 905 removed outlier: 3.620A pdb=" N ASP A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 946 removed outlier: 4.156A pdb=" N TYR A 921 " --> pdb=" O ASN A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 954 removed outlier: 4.126A pdb=" N ASN A 951 " --> pdb=" O GLY A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 1002 removed outlier: 4.032A pdb=" N ASN A 961 " --> pdb=" O THR A 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 145 through 155 removed outlier: 3.504A pdb=" N GLU B 150 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 removed outlier: 3.525A pdb=" N GLY B 245 " --> pdb=" O GLY B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.679A pdb=" N TYR B 304 " --> pdb=" O ARG B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 343 Processing helix chain 'B' and resid 352 through 355 removed outlier: 3.652A pdb=" N LYS B 355 " --> pdb=" O ASP B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 355' Processing helix chain 'B' and resid 370 through 381 Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.877A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 451 " --> pdb=" O TRP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 457 removed outlier: 3.548A pdb=" N VAL B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 485 removed outlier: 3.878A pdb=" N ASP B 485 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 4.793A pdb=" N LYS B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) Proline residue: B 526 - end of helix Processing helix chain 'B' and resid 545 through 550 removed outlier: 3.586A pdb=" N LEU B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 550 " --> pdb=" O PHE B 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 550' Processing helix chain 'B' and resid 557 through 569 removed outlier: 4.053A pdb=" N GLY B 565 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU B 566 " --> pdb=" O TYR B 562 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 593 through 598 Processing helix chain 'B' and resid 599 through 602 Processing helix chain 'B' and resid 603 through 613 removed outlier: 4.221A pdb=" N LEU B 607 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 608 " --> pdb=" O ASP B 604 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE B 609 " --> pdb=" O ARG B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 661 removed outlier: 4.094A pdb=" N ARG B 646 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP B 647 " --> pdb=" O GLN B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 667 removed outlier: 3.560A pdb=" N VAL B 665 " --> pdb=" O PHE B 662 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 667 " --> pdb=" O LYS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 694 removed outlier: 3.503A pdb=" N PHE B 694 " --> pdb=" O ILE B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.576A pdb=" N LEU B 710 " --> pdb=" O LEU B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 745 Processing helix chain 'B' and resid 750 through 787 removed outlier: 3.938A pdb=" N TYR B 754 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 798 Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.941A pdb=" N ALA B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 831 removed outlier: 3.524A pdb=" N SER B 831 " --> pdb=" O HIS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 853 Proline residue: B 840 - end of helix removed outlier: 3.502A pdb=" N VAL B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 846 " --> pdb=" O TYR B 842 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN B 847 " --> pdb=" O VAL B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 905 removed outlier: 3.620A pdb=" N ASP B 905 " --> pdb=" O GLU B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 946 removed outlier: 4.156A pdb=" N TYR B 921 " --> pdb=" O ASN B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 954 removed outlier: 4.126A pdb=" N ASN B 951 " --> pdb=" O GLY B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 1002 removed outlier: 4.032A pdb=" N ASN B 961 " --> pdb=" O THR B 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 239 through 240 removed outlier: 3.596A pdb=" N ASP B 882 " --> pdb=" O LYS B 874 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 874 " --> pdb=" O ASP B 882 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG A 391 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 875 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 252 removed outlier: 7.781A pdb=" N PHE A 279 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR A 405 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 429 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 318 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET A 313 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N LEU A 464 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 315 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 541 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY A 493 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ARG A 622 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA A 491 " --> pdb=" O ARG A 622 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS A 624 " --> pdb=" O ALA A 491 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY A 493 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER A 626 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ILE A 495 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ARG A 628 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N THR A 497 " --> pdb=" O ARG A 628 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU A 630 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 413 removed outlier: 7.201A pdb=" N LYS A 419 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 240 removed outlier: 3.596A pdb=" N ASP A 882 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 874 " --> pdb=" O ASP A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 248 through 252 removed outlier: 7.781A pdb=" N PHE B 279 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR B 405 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN B 429 " --> pdb=" O ILE B 357 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 318 " --> pdb=" O VAL B 362 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET B 313 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 464 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 315 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 541 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY B 493 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ARG B 622 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 491 " --> pdb=" O ARG B 622 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS B 624 " --> pdb=" O ALA B 491 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY B 493 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N SER B 626 " --> pdb=" O GLY B 493 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N ILE B 495 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N ARG B 628 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 10.031A pdb=" N THR B 497 " --> pdb=" O ARG B 628 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU B 630 " --> pdb=" O THR B 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 409 through 413 removed outlier: 7.201A pdb=" N LYS B 419 " --> pdb=" O SER B 411 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 2103 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: 6.75 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12544 1.03 - 1.22: 40 1.22 - 1.42: 5732 1.42 - 1.61: 7562 1.61 - 1.81: 104 Bond restraints: 25982 Sorted by residual: bond pdb=" C21 3PE A1204 " pdb=" O21 3PE A1204 " ideal model delta sigma weight residual 1.316 1.404 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C21 3PE B1204 " pdb=" O21 3PE B1204 " ideal model delta sigma weight residual 1.316 1.404 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C21 3PE B1201 " pdb=" O21 3PE B1201 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C21 3PE A1201 " pdb=" O21 3PE A1201 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C21 3PE B1202 " pdb=" O21 3PE B1202 " ideal model delta sigma weight residual 1.316 1.400 -0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 25977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 46297 2.88 - 5.75: 232 5.75 - 8.63: 41 8.63 - 11.50: 8 11.50 - 14.38: 8 Bond angle restraints: 46586 Sorted by residual: angle pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" O THR B 947 " ideal model delta sigma weight residual 120.24 114.61 5.63 1.11e+00 8.12e-01 2.57e+01 angle pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" O THR A 947 " ideal model delta sigma weight residual 120.24 114.67 5.57 1.11e+00 8.12e-01 2.52e+01 angle pdb=" O12 3PE A1202 " pdb=" P 3PE A1202 " pdb=" O14 3PE A1202 " ideal model delta sigma weight residual 123.79 109.41 14.38 3.00e+00 1.11e-01 2.30e+01 angle pdb=" O12 3PE B1202 " pdb=" P 3PE B1202 " pdb=" O14 3PE B1202 " ideal model delta sigma weight residual 123.79 109.43 14.36 3.00e+00 1.11e-01 2.29e+01 angle pdb=" O12 3PE A1203 " pdb=" P 3PE A1203 " pdb=" O14 3PE A1203 " ideal model delta sigma weight residual 123.79 109.61 14.18 3.00e+00 1.11e-01 2.23e+01 ... (remaining 46581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11726 17.80 - 35.61: 482 35.61 - 53.41: 175 53.41 - 71.21: 57 71.21 - 89.02: 12 Dihedral angle restraints: 12452 sinusoidal: 6612 harmonic: 5840 Sorted by residual: dihedral pdb=" CA ASN A 443 " pdb=" CB ASN A 443 " pdb=" CG ASN A 443 " pdb=" OD1 ASN A 443 " ideal model delta sinusoidal sigma weight residual 120.00 -167.71 -72.29 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CA ASN B 443 " pdb=" CB ASN B 443 " pdb=" CG ASN B 443 " pdb=" OD1 ASN B 443 " ideal model delta sinusoidal sigma weight residual 120.00 -167.71 -72.29 2 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" O21 3PE B1202 " pdb=" C2 3PE B1202 " pdb=" C3 3PE B1202 " pdb=" O31 3PE B1202 " ideal model delta sinusoidal sigma weight residual 60.47 -23.69 84.16 1 3.00e+01 1.11e-03 9.58e+00 ... (remaining 12449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1364 0.030 - 0.060: 388 0.060 - 0.090: 144 0.090 - 0.119: 73 0.119 - 0.149: 21 Chirality restraints: 1990 Sorted by residual: chirality pdb=" C2 3PE B1204 " pdb=" C1 3PE B1204 " pdb=" C3 3PE B1204 " pdb=" O21 3PE B1204 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" C2 3PE A1204 " pdb=" C1 3PE A1204 " pdb=" C3 3PE A1204 " pdb=" O21 3PE A1204 " both_signs ideal model delta sigma weight residual False -2.53 -2.38 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA ILE B 306 " pdb=" N ILE B 306 " pdb=" C ILE B 306 " pdb=" CB ILE B 306 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 1987 not shown) Planarity restraints: 3794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 945 " 0.011 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" N GLU A 946 " -0.034 2.00e-02 2.50e+03 pdb=" CA GLU A 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU A 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 945 " 0.011 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" N GLU B 946 " -0.033 2.00e-02 2.50e+03 pdb=" CA GLU B 946 " 0.009 2.00e-02 2.50e+03 pdb=" H GLU B 946 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 943 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" N VAL A 944 " -0.030 2.00e-02 2.50e+03 pdb=" CA VAL A 944 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL A 944 " 0.013 2.00e-02 2.50e+03 ... (remaining 3791 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1683 2.22 - 2.82: 54330 2.82 - 3.41: 67200 3.41 - 4.01: 89637 4.01 - 4.60: 142158 Nonbonded interactions: 355008 Sorted by model distance: nonbonded pdb=" O GLY A 593 " pdb=" HG SER A 597 " model vdw 1.629 2.450 nonbonded pdb=" O GLY B 593 " pdb=" HG SER B 597 " model vdw 1.630 2.450 nonbonded pdb=" OE1 GLU B 341 " pdb=" HG SER B 353 " model vdw 1.640 2.450 nonbonded pdb=" OE1 GLU A 341 " pdb=" HG SER A 353 " model vdw 1.641 2.450 nonbonded pdb=" O VAL B 665 " pdb=" HG SER B 668 " model vdw 1.679 2.450 ... (remaining 355003 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 35.910 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13414 Z= 0.213 Angle : 0.752 14.381 18120 Z= 0.321 Chirality : 0.039 0.149 1990 Planarity : 0.002 0.022 2250 Dihedral : 11.528 89.015 4950 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.15 % Allowed : 1.62 % Favored : 98.23 % 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: 1.82 (0.21), residues: 1588 helix: 2.60 (0.18), residues: 828 sheet: 0.96 (0.45), residues: 144 loop : -0.74 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 372 TYR 0.009 0.001 TYR A 731 PHE 0.012 0.001 PHE A 984 TRP 0.011 0.001 TRP B 933 HIS 0.003 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00417 (13414) covalent geometry : angle 0.75225 (18120) hydrogen bonds : bond 0.12390 ( 727) hydrogen bonds : angle 4.97253 ( 2103) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6569 (mt0) cc_final: 0.6071 (mm110) REVERT: A 440 LYS cc_start: 0.8906 (mttt) cc_final: 0.8620 (mttp) REVERT: B 149 GLN cc_start: 0.6654 (mt0) cc_final: 0.6132 (mm110) REVERT: B 440 LYS cc_start: 0.8902 (mttt) cc_final: 0.8619 (mttp) REVERT: B 480 LYS cc_start: 0.8348 (tttp) cc_final: 0.8136 (tptp) outliers start: 2 outliers final: 0 residues processed: 187 average time/residue: 1.1291 time to fit residues: 232.7827 Evaluate side-chains 111 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.142580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.097778 restraints weight = 43503.647| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.27 r_work: 0.3006 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13414 Z= 0.114 Angle : 0.446 6.348 18120 Z= 0.236 Chirality : 0.038 0.144 1990 Planarity : 0.003 0.027 2250 Dihedral : 9.826 96.134 2042 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.03 % Allowed : 7.51 % Favored : 91.46 % 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: 2.02 (0.21), residues: 1588 helix: 2.76 (0.18), residues: 854 sheet: 0.90 (0.44), residues: 144 loop : -0.76 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.011 0.001 TYR B 511 PHE 0.009 0.001 PHE A 984 TRP 0.008 0.001 TRP B 933 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd covalent geometry : bond 0.00240 (13414) covalent geometry : angle 0.44578 (18120) hydrogen bonds : bond 0.05311 ( 727) hydrogen bonds : angle 4.19953 ( 2103) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6365 (mt0) cc_final: 0.5692 (mm110) REVERT: A 440 LYS cc_start: 0.8916 (mttt) cc_final: 0.8588 (mttp) REVERT: B 149 GLN cc_start: 0.6388 (mt0) cc_final: 0.5703 (mm110) REVERT: B 480 LYS cc_start: 0.8494 (tttp) cc_final: 0.8185 (tptp) REVERT: B 502 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6518 (mtm180) outliers start: 14 outliers final: 9 residues processed: 122 average time/residue: 0.9291 time to fit residues: 128.3349 Evaluate side-chains 110 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 502 ARG Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 429 GLN B 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.093197 restraints weight = 43581.731| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.16 r_work: 0.2934 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13414 Z= 0.172 Angle : 0.461 4.826 18120 Z= 0.247 Chirality : 0.039 0.147 1990 Planarity : 0.003 0.030 2250 Dihedral : 10.045 92.369 2042 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.96 % Allowed : 7.66 % Favored : 91.38 % 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: 1.92 (0.21), residues: 1588 helix: 2.58 (0.17), residues: 868 sheet: 0.87 (0.44), residues: 144 loop : -0.72 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR A 264 PHE 0.014 0.001 PHE A 984 TRP 0.008 0.001 TRP A 933 HIS 0.003 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00409 (13414) covalent geometry : angle 0.46120 (18120) hydrogen bonds : bond 0.05705 ( 727) hydrogen bonds : angle 4.17291 ( 2103) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6485 (mt0) cc_final: 0.5768 (mm110) REVERT: A 391 ARG cc_start: 0.8300 (mtp85) cc_final: 0.8057 (mtp85) REVERT: A 775 MET cc_start: 0.8344 (mtm) cc_final: 0.7964 (mtp) REVERT: B 149 GLN cc_start: 0.6600 (mt0) cc_final: 0.5890 (mm110) REVERT: B 480 LYS cc_start: 0.8535 (tttp) cc_final: 0.8231 (tptp) REVERT: B 775 MET cc_start: 0.8298 (mtm) cc_final: 0.7876 (mtp) outliers start: 13 outliers final: 12 residues processed: 121 average time/residue: 0.9843 time to fit residues: 133.5939 Evaluate side-chains 115 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.091211 restraints weight = 43550.103| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.26 r_work: 0.2899 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13414 Z= 0.162 Angle : 0.452 5.828 18120 Z= 0.243 Chirality : 0.039 0.154 1990 Planarity : 0.003 0.030 2250 Dihedral : 9.983 90.231 2042 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 8.03 % Favored : 90.43 % 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: 1.85 (0.21), residues: 1588 helix: 2.57 (0.17), residues: 866 sheet: 0.74 (0.44), residues: 144 loop : -0.79 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.011 0.001 TYR B 511 PHE 0.014 0.001 PHE B 984 TRP 0.008 0.001 TRP B 976 HIS 0.004 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00380 (13414) covalent geometry : angle 0.45211 (18120) hydrogen bonds : bond 0.05555 ( 727) hydrogen bonds : angle 4.13902 ( 2103) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6632 (mt0) cc_final: 0.5866 (mm110) REVERT: A 391 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8124 (mtp85) REVERT: A 775 MET cc_start: 0.8390 (mtm) cc_final: 0.7982 (mtp) REVERT: B 149 GLN cc_start: 0.6655 (mt0) cc_final: 0.5876 (mm110) REVERT: B 480 LYS cc_start: 0.8631 (tttp) cc_final: 0.8326 (tptp) REVERT: B 775 MET cc_start: 0.8401 (mtm) cc_final: 0.7999 (mtp) outliers start: 21 outliers final: 10 residues processed: 130 average time/residue: 0.9105 time to fit residues: 133.7762 Evaluate side-chains 112 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 989 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 989 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 152 optimal weight: 2.9990 chunk 67 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.088582 restraints weight = 43822.243| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.24 r_work: 0.2856 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13414 Z= 0.228 Angle : 0.502 5.486 18120 Z= 0.269 Chirality : 0.040 0.151 1990 Planarity : 0.003 0.031 2250 Dihedral : 10.617 87.233 2042 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.02 % Favored : 96.85 % Rotamer: Outliers : 0.81 % Allowed : 8.76 % Favored : 90.43 % 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: 1.66 (0.21), residues: 1588 helix: 2.44 (0.17), residues: 854 sheet: 0.53 (0.44), residues: 148 loop : -0.82 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 446 TYR 0.012 0.002 TYR B 511 PHE 0.019 0.002 PHE B 984 TRP 0.008 0.001 TRP A 933 HIS 0.005 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00553 (13414) covalent geometry : angle 0.50163 (18120) hydrogen bonds : bond 0.06256 ( 727) hydrogen bonds : angle 4.25104 ( 2103) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6678 (mt0) cc_final: 0.5932 (mm110) REVERT: A 775 MET cc_start: 0.8418 (mtm) cc_final: 0.7973 (mtp) REVERT: B 149 GLN cc_start: 0.6692 (mt0) cc_final: 0.5962 (mm110) REVERT: B 480 LYS cc_start: 0.8563 (tttp) cc_final: 0.8279 (tptp) REVERT: B 775 MET cc_start: 0.8410 (mtm) cc_final: 0.7960 (mtp) outliers start: 11 outliers final: 10 residues processed: 114 average time/residue: 1.0028 time to fit residues: 128.8763 Evaluate side-chains 109 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 989 CYS Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090941 restraints weight = 43464.765| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.21 r_work: 0.2897 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13414 Z= 0.122 Angle : 0.437 5.725 18120 Z= 0.234 Chirality : 0.038 0.144 1990 Planarity : 0.003 0.032 2250 Dihedral : 10.224 85.827 2042 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.61 % Rotamer: Outliers : 0.81 % Allowed : 8.69 % Favored : 90.50 % 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: 1.82 (0.21), residues: 1588 helix: 2.59 (0.18), residues: 854 sheet: 0.57 (0.44), residues: 148 loop : -0.79 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.010 0.001 TYR B 511 PHE 0.012 0.001 PHE B 984 TRP 0.009 0.001 TRP B 976 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00275 (13414) covalent geometry : angle 0.43666 (18120) hydrogen bonds : bond 0.05271 ( 727) hydrogen bonds : angle 4.09982 ( 2103) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6632 (mt0) cc_final: 0.5914 (mm110) REVERT: A 604 ASP cc_start: 0.8174 (m-30) cc_final: 0.7822 (p0) REVERT: A 775 MET cc_start: 0.8326 (mtm) cc_final: 0.7893 (mtp) REVERT: A 901 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7112 (tp30) REVERT: B 149 GLN cc_start: 0.6663 (mt0) cc_final: 0.5924 (mm110) REVERT: B 480 LYS cc_start: 0.8498 (tttp) cc_final: 0.8173 (tptp) REVERT: B 604 ASP cc_start: 0.8194 (m-30) cc_final: 0.7834 (p0) REVERT: B 775 MET cc_start: 0.8330 (mtm) cc_final: 0.7898 (mtp) REVERT: B 901 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7106 (tp30) outliers start: 11 outliers final: 8 residues processed: 116 average time/residue: 0.9527 time to fit residues: 124.8099 Evaluate side-chains 106 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089271 restraints weight = 43692.223| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.22 r_work: 0.2867 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13414 Z= 0.179 Angle : 0.465 5.067 18120 Z= 0.249 Chirality : 0.039 0.148 1990 Planarity : 0.003 0.031 2250 Dihedral : 10.551 82.056 2042 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.53 % Favored : 96.35 % Rotamer: Outliers : 0.88 % Allowed : 8.62 % Favored : 90.50 % 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: 1.73 (0.21), residues: 1588 helix: 2.52 (0.18), residues: 854 sheet: 0.50 (0.44), residues: 148 loop : -0.81 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 446 TYR 0.012 0.001 TYR B 511 PHE 0.015 0.001 PHE B 984 TRP 0.008 0.001 TRP A 933 HIS 0.004 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00432 (13414) covalent geometry : angle 0.46451 (18120) hydrogen bonds : bond 0.05682 ( 727) hydrogen bonds : angle 4.13025 ( 2103) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6730 (mt0) cc_final: 0.6073 (mm110) REVERT: A 604 ASP cc_start: 0.8172 (m-30) cc_final: 0.7854 (p0) REVERT: A 775 MET cc_start: 0.8411 (mtm) cc_final: 0.7985 (mtp) REVERT: B 149 GLN cc_start: 0.6749 (mt0) cc_final: 0.6028 (mm110) REVERT: B 480 LYS cc_start: 0.8517 (tttp) cc_final: 0.8192 (tptp) REVERT: B 604 ASP cc_start: 0.8180 (m-30) cc_final: 0.7858 (p0) REVERT: B 775 MET cc_start: 0.8416 (mtm) cc_final: 0.7988 (mtp) outliers start: 12 outliers final: 11 residues processed: 114 average time/residue: 1.0015 time to fit residues: 128.5582 Evaluate side-chains 109 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091426 restraints weight = 43742.699| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.31 r_work: 0.2862 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13414 Z= 0.161 Angle : 0.455 4.937 18120 Z= 0.245 Chirality : 0.039 0.147 1990 Planarity : 0.003 0.031 2250 Dihedral : 10.708 77.842 2042 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.64 % Favored : 97.23 % Rotamer: Outliers : 0.96 % Allowed : 8.47 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.72 (0.21), residues: 1588 helix: 2.52 (0.18), residues: 854 sheet: 0.48 (0.44), residues: 148 loop : -0.81 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.014 0.001 PHE A 984 TRP 0.008 0.001 TRP A 933 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00383 (13414) covalent geometry : angle 0.45542 (18120) hydrogen bonds : bond 0.05514 ( 727) hydrogen bonds : angle 4.09744 ( 2103) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6717 (mt0) cc_final: 0.5803 (mm110) REVERT: A 153 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6890 (mp10) REVERT: A 604 ASP cc_start: 0.8179 (m-30) cc_final: 0.7970 (p0) REVERT: A 775 MET cc_start: 0.8382 (mtm) cc_final: 0.7955 (mtp) REVERT: A 901 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7164 (tp30) REVERT: B 149 GLN cc_start: 0.6713 (mt0) cc_final: 0.5813 (mm110) REVERT: B 153 GLN cc_start: 0.7433 (tm-30) cc_final: 0.6920 (mp10) REVERT: B 480 LYS cc_start: 0.8499 (tttp) cc_final: 0.8175 (tptp) REVERT: B 604 ASP cc_start: 0.8191 (m-30) cc_final: 0.7973 (p0) REVERT: B 775 MET cc_start: 0.8396 (mtm) cc_final: 0.7967 (mtp) REVERT: B 901 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7158 (tp30) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 1.0164 time to fit residues: 126.7677 Evaluate side-chains 107 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092063 restraints weight = 43826.158| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.29 r_work: 0.2872 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13414 Z= 0.136 Angle : 0.442 4.763 18120 Z= 0.236 Chirality : 0.038 0.146 1990 Planarity : 0.003 0.031 2250 Dihedral : 10.471 77.843 2042 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 0.88 % Allowed : 8.76 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.21), residues: 1588 helix: 2.57 (0.18), residues: 854 sheet: 0.53 (0.44), residues: 148 loop : -0.81 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.013 0.001 PHE A 984 TRP 0.008 0.001 TRP B 976 HIS 0.002 0.001 HIS B 679 Details of bonding type rmsd covalent geometry : bond 0.00318 (13414) covalent geometry : angle 0.44238 (18120) hydrogen bonds : bond 0.05197 ( 727) hydrogen bonds : angle 4.02965 ( 2103) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6772 (mt0) cc_final: 0.6159 (mm110) REVERT: A 775 MET cc_start: 0.8382 (mtm) cc_final: 0.7950 (mtp) REVERT: B 149 GLN cc_start: 0.6773 (mt0) cc_final: 0.6158 (mm110) REVERT: B 480 LYS cc_start: 0.8495 (tttp) cc_final: 0.8177 (tptp) REVERT: B 775 MET cc_start: 0.8386 (mtm) cc_final: 0.7950 (mtp) outliers start: 12 outliers final: 11 residues processed: 117 average time/residue: 0.9687 time to fit residues: 127.7998 Evaluate side-chains 111 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 133 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092334 restraints weight = 43670.244| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.20 r_work: 0.2877 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13414 Z= 0.142 Angle : 0.449 4.944 18120 Z= 0.240 Chirality : 0.038 0.132 1990 Planarity : 0.003 0.030 2250 Dihedral : 10.348 77.773 2042 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.17 % Rotamer: Outliers : 0.81 % Allowed : 9.13 % Favored : 90.06 % 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: 1.77 (0.21), residues: 1588 helix: 2.59 (0.18), residues: 852 sheet: 0.50 (0.44), residues: 148 loop : -0.84 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.013 0.001 PHE A 984 TRP 0.008 0.001 TRP B 976 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00332 (13414) covalent geometry : angle 0.44935 (18120) hydrogen bonds : bond 0.05223 ( 727) hydrogen bonds : angle 4.02080 ( 2103) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Residue SER 171 is missing expected H atoms. Skipping. Residue TYR 172 is missing expected H atoms. Skipping. Residue LYS 713 is missing expected H atoms. Skipping. Residue THR 788 is missing expected H atoms. Skipping. Residue LYS 862 is missing expected H atoms. Skipping. Residue LYS 868 is missing expected H atoms. Skipping. Residue LYS 874 is missing expected H atoms. Skipping. Residue VAL 885 is missing expected H atoms. Skipping. Residue LYS 912 is missing expected H atoms. Skipping. Residue VAL 913 is missing expected H atoms. Skipping. Residue LEU 914 is missing expected H atoms. Skipping. Residue LEU 945 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 149 GLN cc_start: 0.6764 (mt0) cc_final: 0.5933 (mm110) REVERT: A 153 GLN cc_start: 0.7537 (tm-30) cc_final: 0.6930 (mp10) REVERT: A 775 MET cc_start: 0.8378 (mtm) cc_final: 0.7942 (mtp) REVERT: A 901 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7169 (tp30) REVERT: B 149 GLN cc_start: 0.6777 (mt0) cc_final: 0.5951 (mm110) REVERT: B 153 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6941 (mp10) REVERT: B 480 LYS cc_start: 0.8493 (tttp) cc_final: 0.8180 (tptp) REVERT: B 775 MET cc_start: 0.8379 (mtm) cc_final: 0.7939 (mtp) outliers start: 11 outliers final: 11 residues processed: 109 average time/residue: 1.0073 time to fit residues: 123.2773 Evaluate side-chains 109 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 699 TYR Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 779 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.092018 restraints weight = 43399.955| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.24 r_work: 0.2880 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13414 Z= 0.134 Angle : 0.442 4.668 18120 Z= 0.236 Chirality : 0.038 0.129 1990 Planarity : 0.003 0.030 2250 Dihedral : 10.175 78.083 2042 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.66 % Rotamer: Outliers : 0.81 % Allowed : 9.06 % Favored : 90.13 % 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: 1.80 (0.21), residues: 1588 helix: 2.62 (0.18), residues: 850 sheet: 0.48 (0.44), residues: 148 loop : -0.83 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 446 TYR 0.011 0.001 TYR B 511 PHE 0.012 0.001 PHE A 984 TRP 0.008 0.001 TRP B 976 HIS 0.003 0.001 HIS A 679 Details of bonding type rmsd covalent geometry : bond 0.00312 (13414) covalent geometry : angle 0.44186 (18120) hydrogen bonds : bond 0.05112 ( 727) hydrogen bonds : angle 3.99453 ( 2103) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7094.96 seconds wall clock time: 120 minutes 32.43 seconds (7232.43 seconds total)