Starting phenix.real_space_refine on Sat Jan 18 01:10:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.map" model { file = "/net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ask_43817/01_2025/9ask_43817.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 7414 2.51 5 N 1978 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 11564 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 5782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5782 Classifications: {'peptide': 741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 21, 'TRANS': 719} Chain breaks: 8 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 7.21, per 1000 atoms: 0.62 Number of scatterers: 11564 At special positions: 0 Unit cell: (153.64, 102.12, 84.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2098 8.00 N 1978 7.00 C 7414 6.00 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: 2.73 Conformation dependent library (CDL) restraints added in 1.6 seconds 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 10 sheets defined 56.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.740A pdb=" N GLY A 120 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 removed outlier: 4.062A pdb=" N ALA A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 162 Processing helix chain 'A' and resid 191 through 204 removed outlier: 3.870A pdb=" N GLY A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.910A pdb=" N GLY A 222 " --> pdb=" O HIS A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.697A pdb=" N LEU A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.968A pdb=" N LEU A 329 " --> pdb=" O HIS A 325 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N CYS A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 365 removed outlier: 4.039A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.724A pdb=" N LYS A 407 " --> pdb=" O SER A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.512A pdb=" N ILE A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.504A pdb=" N LEU A 446 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 448 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 479 removed outlier: 3.720A pdb=" N GLN A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 510 removed outlier: 4.129A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 506 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU A 507 " --> pdb=" O LYS A 503 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 540 removed outlier: 4.307A pdb=" N ARG A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 536 " --> pdb=" O ILE A 532 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.559A pdb=" N ALA A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.635A pdb=" N MET A 563 " --> pdb=" O LEU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 592 removed outlier: 3.609A pdb=" N VAL A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N TRP A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.540A pdb=" N LEU A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 636 removed outlier: 3.671A pdb=" N LEU A 629 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 679 through 687 removed outlier: 4.055A pdb=" N VAL A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 685 " --> pdb=" O LYS A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 3.675A pdb=" N ARG A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 742 Processing helix chain 'A' and resid 744 through 769 removed outlier: 3.995A pdb=" N SER A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 758 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 764 " --> pdb=" O GLY A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 779 Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.506A pdb=" N LEU A 785 " --> pdb=" O PHE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 817 through 822 removed outlier: 3.531A pdb=" N ALA A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.141A pdb=" N VAL A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 832 " --> pdb=" O GLU A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 890 removed outlier: 3.730A pdb=" N LEU A 887 " --> pdb=" O ALA A 883 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 890 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 94 through 101 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 136 removed outlier: 4.488A pdb=" N VAL B 124 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 162 Processing helix chain 'B' and resid 191 through 204 removed outlier: 3.827A pdb=" N GLY B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 removed outlier: 3.931A pdb=" N GLY B 222 " --> pdb=" O HIS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 245 removed outlier: 3.676A pdb=" N LEU B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.674A pdb=" N LEU B 329 " --> pdb=" O HIS B 325 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS B 335 " --> pdb=" O TYR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 367 removed outlier: 3.739A pdb=" N ASN B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.645A pdb=" N LYS B 407 " --> pdb=" O SER B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.551A pdb=" N ILE B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.575A pdb=" N LEU B 446 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 478 removed outlier: 3.568A pdb=" N GLN B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 510 removed outlier: 4.103A pdb=" N LYS B 503 " --> pdb=" O SER B 499 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 506 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 507 " --> pdb=" O LYS B 503 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 540 removed outlier: 4.364A pdb=" N ARG B 533 " --> pdb=" O GLY B 529 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.541A pdb=" N ALA B 555 " --> pdb=" O HIS B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.654A pdb=" N MET B 563 " --> pdb=" O LEU B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 592 removed outlier: 3.881A pdb=" N VAL B 586 " --> pdb=" O ILE B 582 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 622 removed outlier: 3.524A pdb=" N LEU B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 635 removed outlier: 3.655A pdb=" N LEU B 629 " --> pdb=" O PRO B 625 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 653 Processing helix chain 'B' and resid 665 through 676 Processing helix chain 'B' and resid 679 through 687 removed outlier: 4.047A pdb=" N VAL B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 684 " --> pdb=" O MET B 680 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 685 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 729 removed outlier: 3.642A pdb=" N ARG B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 744 through 769 removed outlier: 3.981A pdb=" N SER B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 758 " --> pdb=" O SER B 754 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 764 " --> pdb=" O GLY B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 779 Processing helix chain 'B' and resid 780 through 788 removed outlier: 3.554A pdb=" N LEU B 785 " --> pdb=" O PHE B 781 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 787 " --> pdb=" O LYS B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 799 Processing helix chain 'B' and resid 807 through 813 Processing helix chain 'B' and resid 817 through 822 removed outlier: 3.514A pdb=" N ALA B 822 " --> pdb=" O VAL B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 835 removed outlier: 4.146A pdb=" N VAL B 831 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE B 832 " --> pdb=" O GLU B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 890 removed outlier: 3.733A pdb=" N LEU B 887 " --> pdb=" O ALA B 883 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 890 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 169 removed outlier: 7.501A pdb=" N ALA A 140 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N CYS A 189 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE A 142 " --> pdb=" O CYS A 189 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS A 139 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A 212 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 264 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 112 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 283 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 309 through 312 removed outlier: 4.047A pdb=" N ARG A 311 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 293 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 494 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 295 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 457 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 495 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 459 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 341 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 464 Processing sheet with id=AA4, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.607A pdb=" N HIS A 610 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 598 " --> pdb=" O VAL A 608 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 608 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AA6, first strand: chain 'B' and resid 168 through 169 removed outlier: 7.539A pdb=" N ALA B 140 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N CYS B 189 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE B 142 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL B 112 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR B 283 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 309 through 312 removed outlier: 4.041A pdb=" N ARG B 311 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 457 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 341 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 463 through 464 removed outlier: 3.512A pdb=" N ARG B 467 " --> pdb=" O PHE B 464 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 595 through 598 removed outlier: 3.573A pdb=" N HIS B 610 " --> pdb=" O GLN B 596 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 598 " --> pdb=" O VAL B 608 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 608 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 862 through 863 499 hydrogen bonds defined for protein. 1422 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: 3.73 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3758 1.34 - 1.46: 2552 1.46 - 1.58: 5336 1.58 - 1.70: 0 1.70 - 1.82: 118 Bond restraints: 11764 Sorted by residual: bond pdb=" CA ILE B 166 " pdb=" CB ILE B 166 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.71e+00 bond pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.58e+00 bond pdb=" CB ASN B 270 " pdb=" CG ASN B 270 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.52e+00 bond pdb=" CB ARG A 242 " pdb=" CG ARG A 242 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" SD MET A 477 " pdb=" CE MET A 477 " ideal model delta sigma weight residual 1.791 1.767 0.024 2.50e-02 1.60e+03 9.44e-01 ... (remaining 11759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15638 1.98 - 3.96: 222 3.96 - 5.93: 38 5.93 - 7.91: 9 7.91 - 9.89: 5 Bond angle restraints: 15912 Sorted by residual: angle pdb=" CB MET B 477 " pdb=" CG MET B 477 " pdb=" SD MET B 477 " ideal model delta sigma weight residual 112.70 102.81 9.89 3.00e+00 1.11e-01 1.09e+01 angle pdb=" CB ARG A 242 " pdb=" CG ARG A 242 " pdb=" CD ARG A 242 " ideal model delta sigma weight residual 111.30 117.79 -6.49 2.30e+00 1.89e-01 7.96e+00 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 104.28 8.42 3.00e+00 1.11e-01 7.88e+00 angle pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " pdb=" CG LEU A 233 " ideal model delta sigma weight residual 116.30 125.95 -9.65 3.50e+00 8.16e-02 7.60e+00 angle pdb=" N VAL B 486 " pdb=" CA VAL B 486 " pdb=" C VAL B 486 " ideal model delta sigma weight residual 111.62 109.54 2.08 7.90e-01 1.60e+00 6.95e+00 ... (remaining 15907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.15: 5909 18.15 - 36.30: 895 36.30 - 54.44: 210 54.44 - 72.59: 43 72.59 - 90.74: 19 Dihedral angle restraints: 7076 sinusoidal: 2790 harmonic: 4286 Sorted by residual: dihedral pdb=" CA ASP B 630 " pdb=" CB ASP B 630 " pdb=" CG ASP B 630 " pdb=" OD1 ASP B 630 " ideal model delta sinusoidal sigma weight residual -30.00 -88.49 58.49 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA ASP A 630 " pdb=" CB ASP A 630 " pdb=" CG ASP A 630 " pdb=" OD1 ASP A 630 " ideal model delta sinusoidal sigma weight residual -30.00 -88.25 58.25 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA LEU A 282 " pdb=" C LEU A 282 " pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta harmonic sigma weight residual 180.00 163.17 16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1109 0.029 - 0.058: 512 0.058 - 0.086: 162 0.086 - 0.115: 74 0.115 - 0.144: 19 Chirality restraints: 1876 Sorted by residual: chirality pdb=" CA ASN A 270 " pdb=" N ASN A 270 " pdb=" C ASN A 270 " pdb=" CB ASN A 270 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA VAL B 732 " pdb=" N VAL B 732 " pdb=" C VAL B 732 " pdb=" CB VAL B 732 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ASN B 270 " pdb=" N ASN B 270 " pdb=" C ASN B 270 " pdb=" CB ASN B 270 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 1873 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 513 " 0.042 5.00e-02 4.00e+02 6.26e-02 6.28e+00 pdb=" N PRO A 514 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 514 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 514 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 513 " -0.041 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 514 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 514 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 514 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 204 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C GLU B 204 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 204 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN B 205 " -0.012 2.00e-02 2.50e+03 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3139 2.80 - 3.32: 11186 3.32 - 3.85: 19097 3.85 - 4.37: 21988 4.37 - 4.90: 36960 Nonbonded interactions: 92370 Sorted by model distance: nonbonded pdb=" NZ LYS B 236 " pdb=" OE1 GLU B 537 " model vdw 2.275 3.120 nonbonded pdb=" O ASP A 549 " pdb=" OG1 THR A 552 " model vdw 2.276 3.040 nonbonded pdb=" OG1 THR B 421 " pdb=" NH1 ARG B 745 " model vdw 2.282 3.120 nonbonded pdb=" OE2 GLU B 424 " pdb=" NH1 ARG B 745 " model vdw 2.292 3.120 nonbonded pdb=" OD2 ASP A 647 " pdb=" NH1 ARG A 784 " model vdw 2.296 3.120 ... (remaining 92365 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: 0.05 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 27.860 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.003 0.035 11764 Z= 0.186 Angle : 0.604 9.891 15912 Z= 0.297 Chirality : 0.040 0.144 1876 Planarity : 0.004 0.063 1990 Dihedral : 18.522 90.740 4292 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.40 % Allowed : 36.10 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.22), residues: 1446 helix: -0.43 (0.20), residues: 696 sheet: -0.02 (0.49), residues: 114 loop : -0.97 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 95 HIS 0.005 0.001 HIS B 417 PHE 0.025 0.001 PHE B 146 TYR 0.029 0.002 TYR A 283 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 238 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 LEU cc_start: 0.8185 (mm) cc_final: 0.7873 (mm) REVERT: B 438 ARG cc_start: 0.6362 (ttm-80) cc_final: 0.6037 (ttm-80) REVERT: B 493 ILE cc_start: 0.8725 (mt) cc_final: 0.8505 (mt) outliers start: 5 outliers final: 2 residues processed: 242 average time/residue: 0.2481 time to fit residues: 85.6404 Evaluate side-chains 190 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 862 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 0.1980 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 134 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN B 195 ASN B 219 HIS B 498 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.209674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177482 restraints weight = 16391.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.182488 restraints weight = 9387.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185898 restraints weight = 6456.724| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11764 Z= 0.195 Angle : 0.624 8.555 15912 Z= 0.311 Chirality : 0.041 0.142 1876 Planarity : 0.004 0.044 1990 Dihedral : 4.334 35.426 1583 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.27 % Allowed : 32.83 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1446 helix: -0.27 (0.18), residues: 790 sheet: -0.01 (0.46), residues: 120 loop : -1.58 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 673 HIS 0.006 0.001 HIS B 417 PHE 0.019 0.001 PHE A 464 TYR 0.025 0.002 TYR A 283 ARG 0.009 0.001 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 199 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6486 (tt0) REVERT: A 154 LYS cc_start: 0.8851 (tptm) cc_final: 0.8619 (tptm) REVERT: A 226 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7435 (ptp90) REVERT: A 264 MET cc_start: 0.6448 (mpp) cc_final: 0.6213 (mpp) REVERT: A 483 ARG cc_start: 0.7266 (mpt-90) cc_final: 0.6699 (mtm-85) REVERT: A 817 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 835 ASN cc_start: 0.7887 (m110) cc_final: 0.7499 (t0) REVERT: B 127 LEU cc_start: 0.8779 (mt) cc_final: 0.8488 (tt) REVERT: B 332 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6517 (tt0) REVERT: B 835 ASN cc_start: 0.7840 (m110) cc_final: 0.7497 (t0) outliers start: 66 outliers final: 39 residues processed: 241 average time/residue: 0.2524 time to fit residues: 86.6416 Evaluate side-chains 220 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 83 optimal weight: 0.1980 chunk 85 optimal weight: 0.0270 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 GLN A 649 HIS ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.209625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.177133 restraints weight = 16493.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.182266 restraints weight = 9456.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185691 restraints weight = 6482.004| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11764 Z= 0.181 Angle : 0.575 7.181 15912 Z= 0.284 Chirality : 0.041 0.161 1876 Planarity : 0.004 0.039 1990 Dihedral : 4.115 19.249 1580 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.71 % Allowed : 33.31 % Favored : 61.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.21), residues: 1446 helix: -0.04 (0.18), residues: 808 sheet: 0.13 (0.43), residues: 130 loop : -1.68 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.005 0.001 HIS B 649 PHE 0.019 0.001 PHE B 343 TYR 0.024 0.002 TYR A 283 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5157 (ppp) cc_final: 0.4760 (ppp) REVERT: A 135 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6673 (tt0) REVERT: A 226 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7354 (ptp90) REVERT: A 308 LYS cc_start: 0.7272 (ttmm) cc_final: 0.6895 (tttm) REVERT: A 483 ARG cc_start: 0.7219 (mpt-90) cc_final: 0.6740 (mtm-85) REVERT: A 493 ILE cc_start: 0.8535 (mt) cc_final: 0.8289 (mt) REVERT: A 798 ARG cc_start: 0.8329 (ttm-80) cc_final: 0.8089 (ttm110) REVERT: A 835 ASN cc_start: 0.7884 (m110) cc_final: 0.7513 (t0) REVERT: B 127 LEU cc_start: 0.8809 (mt) cc_final: 0.8461 (tt) REVERT: B 332 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6610 (tt0) REVERT: B 493 ILE cc_start: 0.8577 (mt) cc_final: 0.8360 (mt) REVERT: B 668 ARG cc_start: 0.7537 (ttp-110) cc_final: 0.7079 (ttt-90) REVERT: B 835 ASN cc_start: 0.7875 (m110) cc_final: 0.7492 (t0) outliers start: 59 outliers final: 39 residues processed: 238 average time/residue: 0.2523 time to fit residues: 85.8136 Evaluate side-chains 219 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 112 optimal weight: 0.0980 chunk 119 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 ASN B 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.209490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.176786 restraints weight = 16531.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181928 restraints weight = 9428.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.185409 restraints weight = 6444.545| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11764 Z= 0.188 Angle : 0.574 10.033 15912 Z= 0.281 Chirality : 0.040 0.136 1876 Planarity : 0.004 0.037 1990 Dihedral : 4.109 18.798 1580 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.91 % Allowed : 33.23 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.21), residues: 1446 helix: 0.08 (0.18), residues: 812 sheet: -0.54 (0.40), residues: 152 loop : -1.66 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 PHE 0.020 0.001 PHE B 146 TYR 0.028 0.001 TYR A 283 ARG 0.004 0.000 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 184 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6674 (tt0) REVERT: A 226 ARG cc_start: 0.7728 (ptp90) cc_final: 0.7407 (ptp90) REVERT: A 308 LYS cc_start: 0.7390 (ttmm) cc_final: 0.7007 (tttm) REVERT: A 487 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.6371 (m-30) REVERT: A 493 ILE cc_start: 0.8559 (mt) cc_final: 0.8310 (mt) REVERT: A 835 ASN cc_start: 0.7894 (m110) cc_final: 0.7479 (t0) REVERT: A 889 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5957 (pt0) REVERT: B 127 LEU cc_start: 0.8808 (mt) cc_final: 0.8468 (tt) REVERT: B 143 ILE cc_start: 0.8179 (mt) cc_final: 0.7964 (mt) REVERT: B 332 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6453 (tt0) REVERT: B 487 ASP cc_start: 0.7102 (OUTLIER) cc_final: 0.6518 (m-30) REVERT: B 680 MET cc_start: 0.6291 (tpp) cc_final: 0.6084 (tpp) REVERT: B 835 ASN cc_start: 0.7866 (m110) cc_final: 0.7464 (t0) REVERT: B 889 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5930 (pt0) outliers start: 74 outliers final: 49 residues processed: 236 average time/residue: 0.2288 time to fit residues: 78.8013 Evaluate side-chains 230 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 10 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.208099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.175013 restraints weight = 16415.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.180065 restraints weight = 9428.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.183495 restraints weight = 6511.782| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11764 Z= 0.200 Angle : 0.582 10.087 15912 Z= 0.281 Chirality : 0.041 0.134 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.136 19.061 1580 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.47 % Allowed : 33.15 % Favored : 60.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.21), residues: 1446 helix: 0.11 (0.18), residues: 818 sheet: -0.52 (0.41), residues: 136 loop : -1.64 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 PHE 0.016 0.001 PHE B 146 TYR 0.023 0.001 TYR A 283 ARG 0.004 0.000 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 181 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5272 (ppp) cc_final: 0.4544 (ppp) REVERT: A 135 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6701 (tt0) REVERT: A 226 ARG cc_start: 0.7752 (ptp90) cc_final: 0.7438 (ptp90) REVERT: A 308 LYS cc_start: 0.7439 (ttmm) cc_final: 0.7057 (tttm) REVERT: A 487 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6294 (m-30) REVERT: A 493 ILE cc_start: 0.8608 (mt) cc_final: 0.8370 (mt) REVERT: A 685 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 835 ASN cc_start: 0.7898 (m110) cc_final: 0.7485 (t0) REVERT: A 889 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5976 (pt0) REVERT: B 127 LEU cc_start: 0.8810 (mt) cc_final: 0.8514 (tt) REVERT: B 332 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6395 (tt0) REVERT: B 680 MET cc_start: 0.6438 (tpp) cc_final: 0.6223 (tpp) REVERT: B 685 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 835 ASN cc_start: 0.7886 (m110) cc_final: 0.7471 (t0) REVERT: B 889 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5940 (pt0) outliers start: 81 outliers final: 56 residues processed: 236 average time/residue: 0.2170 time to fit residues: 75.4334 Evaluate side-chains 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 39 optimal weight: 0.0370 chunk 44 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.210905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.178809 restraints weight = 16575.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183908 restraints weight = 9451.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.187427 restraints weight = 6452.798| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11764 Z= 0.155 Angle : 0.568 9.862 15912 Z= 0.274 Chirality : 0.039 0.135 1876 Planarity : 0.003 0.039 1990 Dihedral : 4.022 19.266 1580 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.80 % Favored : 95.99 % Rotamer: Outliers : 4.79 % Allowed : 34.35 % Favored : 60.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1446 helix: 0.22 (0.18), residues: 820 sheet: -0.38 (0.41), residues: 136 loop : -1.67 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 588 HIS 0.005 0.001 HIS A 416 PHE 0.017 0.001 PHE B 146 TYR 0.019 0.001 TYR B 667 ARG 0.003 0.000 ARG B 396 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7232 (tm-30) cc_final: 0.6703 (tt0) REVERT: A 142 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7406 (t80) REVERT: A 226 ARG cc_start: 0.7693 (ptp90) cc_final: 0.7385 (ptp90) REVERT: A 308 LYS cc_start: 0.7441 (ttmm) cc_final: 0.7035 (tttm) REVERT: A 388 LEU cc_start: 0.6249 (mt) cc_final: 0.6031 (mt) REVERT: A 487 ASP cc_start: 0.6653 (OUTLIER) cc_final: 0.6140 (m-30) REVERT: A 493 ILE cc_start: 0.8571 (mt) cc_final: 0.8357 (mt) REVERT: A 685 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: A 835 ASN cc_start: 0.7897 (m110) cc_final: 0.7474 (t0) REVERT: A 889 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.6002 (pt0) REVERT: B 127 LEU cc_start: 0.8785 (mt) cc_final: 0.8480 (tt) REVERT: B 142 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7582 (t80) REVERT: B 332 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6402 (tt0) REVERT: B 386 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: B 685 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 835 ASN cc_start: 0.7848 (m110) cc_final: 0.7461 (t0) REVERT: B 889 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5961 (pt0) outliers start: 60 outliers final: 40 residues processed: 228 average time/residue: 0.2288 time to fit residues: 75.5734 Evaluate side-chains 225 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 303 TYR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 386 GLU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 662 THR Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 129 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 0.0570 chunk 37 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.207852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175219 restraints weight = 16711.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.180292 restraints weight = 9582.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.183703 restraints weight = 6587.106| |-----------------------------------------------------------------------------| r_work (final): 0.4355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11764 Z= 0.197 Angle : 0.586 9.694 15912 Z= 0.283 Chirality : 0.041 0.144 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.076 18.539 1580 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 5.59 % Allowed : 33.15 % Favored : 61.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.22), residues: 1446 helix: 0.22 (0.18), residues: 820 sheet: -0.55 (0.41), residues: 138 loop : -1.67 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 PHE 0.017 0.001 PHE B 146 TYR 0.019 0.001 TYR A 283 ARG 0.005 0.000 ARG A 798 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 181 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6731 (tt0) REVERT: A 142 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 226 ARG cc_start: 0.7703 (ptp90) cc_final: 0.7405 (ptp90) REVERT: A 242 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7073 (ttp80) REVERT: A 308 LYS cc_start: 0.7483 (ttmm) cc_final: 0.7065 (tttm) REVERT: A 411 TRP cc_start: 0.3533 (OUTLIER) cc_final: 0.3036 (m-10) REVERT: A 487 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.6143 (m-30) REVERT: A 493 ILE cc_start: 0.8653 (mt) cc_final: 0.8444 (mt) REVERT: A 640 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7609 (mmtt) REVERT: A 685 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 835 ASN cc_start: 0.7898 (m110) cc_final: 0.7458 (t0) REVERT: A 889 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.6023 (pt0) REVERT: B 127 LEU cc_start: 0.8804 (mt) cc_final: 0.8510 (tt) REVERT: B 142 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7657 (t80) REVERT: B 204 GLU cc_start: 0.7289 (mp0) cc_final: 0.7032 (pm20) REVERT: B 231 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7204 (tt0) REVERT: B 332 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6587 (tt0) REVERT: B 411 TRP cc_start: 0.3644 (OUTLIER) cc_final: 0.2941 (m-10) REVERT: B 685 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: B 835 ASN cc_start: 0.7920 (m110) cc_final: 0.7495 (t0) REVERT: B 889 GLN cc_start: 0.6235 (OUTLIER) cc_final: 0.6009 (pt0) outliers start: 70 outliers final: 49 residues processed: 226 average time/residue: 0.2365 time to fit residues: 77.0117 Evaluate side-chains 237 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 535 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 139 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 113 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.209212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.176613 restraints weight = 16736.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.181784 restraints weight = 9522.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.185347 restraints weight = 6509.123| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11764 Z= 0.174 Angle : 0.584 12.021 15912 Z= 0.282 Chirality : 0.040 0.175 1876 Planarity : 0.003 0.037 1990 Dihedral : 4.029 18.893 1580 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 5.51 % Allowed : 33.47 % Favored : 61.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1446 helix: 0.23 (0.18), residues: 820 sheet: -0.42 (0.42), residues: 136 loop : -1.68 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.006 0.001 HIS A 417 PHE 0.015 0.001 PHE B 146 TYR 0.017 0.001 TYR A 283 ARG 0.004 0.000 ARG A 798 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6714 (tt0) REVERT: A 142 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7423 (t80) REVERT: A 226 ARG cc_start: 0.7651 (ptp90) cc_final: 0.7341 (ptp90) REVERT: A 308 LYS cc_start: 0.7489 (ttmm) cc_final: 0.7080 (tttm) REVERT: A 487 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6150 (m-30) REVERT: A 493 ILE cc_start: 0.8663 (mt) cc_final: 0.8455 (mt) REVERT: A 640 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7548 (mmtt) REVERT: A 685 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: A 835 ASN cc_start: 0.7926 (m110) cc_final: 0.7497 (t0) REVERT: A 889 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.6000 (pt0) REVERT: B 127 LEU cc_start: 0.8786 (mt) cc_final: 0.8513 (tt) REVERT: B 142 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7620 (t80) REVERT: B 231 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7167 (tt0) REVERT: B 332 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6536 (tt0) REVERT: B 411 TRP cc_start: 0.3572 (OUTLIER) cc_final: 0.2900 (m-10) REVERT: B 685 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.7046 (mp0) REVERT: B 717 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6738 (mmtt) REVERT: B 835 ASN cc_start: 0.7878 (m110) cc_final: 0.7479 (t0) REVERT: B 889 GLN cc_start: 0.6163 (OUTLIER) cc_final: 0.5951 (pt0) outliers start: 69 outliers final: 49 residues processed: 225 average time/residue: 0.2276 time to fit residues: 74.0529 Evaluate side-chains 232 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 173 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 717 LYS Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 141 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.208851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.176214 restraints weight = 16627.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.181358 restraints weight = 9472.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.184920 restraints weight = 6477.235| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11764 Z= 0.189 Angle : 0.590 9.619 15912 Z= 0.285 Chirality : 0.040 0.133 1876 Planarity : 0.003 0.036 1990 Dihedral : 4.040 18.709 1580 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 5.27 % Allowed : 33.63 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1446 helix: 0.24 (0.18), residues: 818 sheet: -0.41 (0.42), residues: 136 loop : -1.70 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 666 HIS 0.006 0.001 HIS A 417 PHE 0.014 0.001 PHE B 146 TYR 0.017 0.001 TYR A 283 ARG 0.005 0.000 ARG B 798 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6840 (tt0) REVERT: A 142 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7397 (t80) REVERT: A 204 GLU cc_start: 0.7235 (mp0) cc_final: 0.6988 (pm20) REVERT: A 226 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7366 (ptp90) REVERT: A 264 MET cc_start: 0.6978 (mpp) cc_final: 0.6707 (mpp) REVERT: A 308 LYS cc_start: 0.7507 (ttmm) cc_final: 0.7092 (tttm) REVERT: A 411 TRP cc_start: 0.3670 (OUTLIER) cc_final: 0.3123 (m-10) REVERT: A 462 PRO cc_start: 0.7885 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: A 487 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: A 685 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 835 ASN cc_start: 0.7936 (m110) cc_final: 0.7493 (t0) REVERT: A 889 GLN cc_start: 0.6254 (OUTLIER) cc_final: 0.6019 (pt0) REVERT: B 127 LEU cc_start: 0.8771 (mt) cc_final: 0.8482 (tt) REVERT: B 142 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 231 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7192 (tt0) REVERT: B 332 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6347 (tt0) REVERT: B 411 TRP cc_start: 0.3585 (OUTLIER) cc_final: 0.2935 (m-10) REVERT: B 685 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 835 ASN cc_start: 0.7912 (m110) cc_final: 0.7481 (t0) REVERT: B 889 GLN cc_start: 0.6174 (OUTLIER) cc_final: 0.5955 (pt0) outliers start: 66 outliers final: 50 residues processed: 222 average time/residue: 0.2226 time to fit residues: 72.3954 Evaluate side-chains 233 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 174 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 889 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 135 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 106 optimal weight: 0.0020 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.207733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.175036 restraints weight = 16567.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180153 restraints weight = 9502.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.183658 restraints weight = 6525.498| |-----------------------------------------------------------------------------| r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11764 Z= 0.200 Angle : 0.607 9.930 15912 Z= 0.291 Chirality : 0.041 0.172 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.096 18.471 1580 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 4.87 % Allowed : 34.35 % Favored : 60.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1446 helix: 0.22 (0.18), residues: 818 sheet: -0.40 (0.42), residues: 136 loop : -1.71 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.006 0.001 HIS A 417 PHE 0.010 0.001 PHE A 146 TYR 0.018 0.001 TYR A 283 ARG 0.006 0.000 ARG A 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2892 Ramachandran restraints generated. 1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6852 (tt0) REVERT: A 142 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7413 (t80) REVERT: A 226 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7372 (ptp90) REVERT: A 242 ARG cc_start: 0.7109 (ttp80) cc_final: 0.6820 (ttp80) REVERT: A 264 MET cc_start: 0.7035 (mpp) cc_final: 0.6775 (mpp) REVERT: A 308 LYS cc_start: 0.7534 (ttmm) cc_final: 0.7094 (tttm) REVERT: A 411 TRP cc_start: 0.3680 (OUTLIER) cc_final: 0.3089 (m-10) REVERT: A 462 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7606 (Cg_exo) REVERT: A 487 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6156 (m-30) REVERT: A 685 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 889 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.6014 (pt0) REVERT: B 127 LEU cc_start: 0.8798 (mt) cc_final: 0.8464 (tt) REVERT: B 142 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7684 (t80) REVERT: B 231 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7214 (tt0) REVERT: B 332 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6318 (tt0) REVERT: B 411 TRP cc_start: 0.3545 (OUTLIER) cc_final: 0.2914 (m-10) REVERT: B 685 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 835 ASN cc_start: 0.7936 (m110) cc_final: 0.7475 (t0) outliers start: 61 outliers final: 53 residues processed: 219 average time/residue: 0.2297 time to fit residues: 74.3791 Evaluate side-chains 235 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 411 TRP Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 422 PHE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 640 LYS Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain A residue 717 LYS Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 889 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 PHE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 360 GLU Chi-restraints excluded: chain B residue 361 PHE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 411 TRP Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 803 ASN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 831 VAL Chi-restraints excluded: chain B residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 55 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.207006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174141 restraints weight = 16538.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.179327 restraints weight = 9530.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.182842 restraints weight = 6538.404| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11764 Z= 0.217 Angle : 0.614 10.125 15912 Z= 0.296 Chirality : 0.041 0.169 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.134 18.643 1580 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.70 % Favored : 95.16 % Rotamer: Outliers : 4.95 % Allowed : 34.42 % Favored : 60.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1446 helix: 0.22 (0.18), residues: 818 sheet: -0.52 (0.42), residues: 140 loop : -1.69 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 411 HIS 0.007 0.001 HIS A 417 PHE 0.009 0.001 PHE A 146 TYR 0.018 0.002 TYR A 283 ARG 0.006 0.000 ARG A 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.77 seconds wall clock time: 67 minutes 3.84 seconds (4023.84 seconds total)