Starting phenix.real_space_refine on Tue Jun 10 09:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ask_43817/06_2025/9ask_43817.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ask_43817/06_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_43817/06_2025/9ask_43817.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ask_43817/06_2025/9ask_43817.map" model { file = "/net/cci-nas-00/data/ceres_data/9ask_43817/06_2025/9ask_43817.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ask_43817/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.85, per 1000 atoms: 0.68 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 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: 1.43 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: 3.67 Time building geometry restraints manager: 3.08 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: 0.06 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: 3.230 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.050 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- 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= 0.122 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 Details of bonding type rmsd hydrogen bonds : bond 0.29238 ( 499) hydrogen bonds : angle 8.63786 ( 1422) covalent geometry : bond 0.00284 (11764) covalent geometry : angle 0.60417 (15912) *********************** 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 : 1.247 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: 0.2331 time to fit residues: 80.7342 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 : 1.180 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.177469 restraints weight = 16392.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.182475 restraints weight = 9388.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.185917 restraints weight = 6458.584| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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= 0.136 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 Details of bonding type rmsd hydrogen bonds : bond 0.05134 ( 499) hydrogen bonds : angle 5.67050 ( 1422) covalent geometry : bond 0.00301 (11764) covalent geometry : angle 0.62369 (15912) *********************** 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 : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6491 (tt0) REVERT: A 154 LYS cc_start: 0.8851 (tptm) cc_final: 0.8616 (tptm) REVERT: A 226 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7439 (ptp90) REVERT: A 264 MET cc_start: 0.6452 (mpp) cc_final: 0.6217 (mpp) REVERT: A 483 ARG cc_start: 0.7266 (mpt-90) cc_final: 0.6696 (mtm-85) REVERT: A 817 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8755 (p) REVERT: A 835 ASN cc_start: 0.7892 (m110) cc_final: 0.7500 (t0) REVERT: B 127 LEU cc_start: 0.8781 (mt) cc_final: 0.8486 (tt) REVERT: B 332 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6524 (tt0) REVERT: B 835 ASN cc_start: 0.7846 (m110) cc_final: 0.7499 (t0) outliers start: 66 outliers final: 39 residues processed: 241 average time/residue: 0.2285 time to fit residues: 78.5931 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 : 1.227 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 83 optimal weight: 0.1980 chunk 85 optimal weight: 0.5980 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 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 = 0.4595 r_free = 0.4595 target = 0.208681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.176174 restraints weight = 16550.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.181211 restraints weight = 9503.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.184617 restraints weight = 6533.534| |-----------------------------------------------------------------------------| r_work (final): 0.4383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2101 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= 0.129 Angle : 0.582 7.485 15912 Z= 0.287 Chirality : 0.041 0.163 1876 Planarity : 0.004 0.039 1990 Dihedral : 4.147 19.135 1580 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.95 % Allowed : 33.39 % Favored : 61.66 % 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: -0.97 (0.21), residues: 1446 helix: -0.06 (0.18), residues: 808 sheet: 0.11 (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 0.020 0.001 PHE B 343 TYR 0.025 0.002 TYR A 283 ARG 0.004 0.000 ARG A 242 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 499) hydrogen bonds : angle 5.12897 ( 1422) covalent geometry : bond 0.00298 (11764) covalent geometry : angle 0.58194 (15912) *********************** 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 257 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5141 (ppp) cc_final: 0.4724 (ppp) REVERT: A 135 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6629 (tt0) REVERT: A 226 ARG cc_start: 0.7736 (ptp90) cc_final: 0.7375 (ptp90) REVERT: A 242 ARG cc_start: 0.7073 (ttp80) cc_final: 0.6857 (ttp80) REVERT: A 483 ARG cc_start: 0.7254 (mpt-90) cc_final: 0.6771 (mtm-85) REVERT: A 493 ILE cc_start: 0.8561 (mt) cc_final: 0.8310 (mt) REVERT: A 798 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.8088 (ttm110) REVERT: A 835 ASN cc_start: 0.7871 (m110) cc_final: 0.7506 (t0) REVERT: B 127 LEU cc_start: 0.8815 (mt) cc_final: 0.8467 (tt) REVERT: B 332 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6605 (tt0) REVERT: B 493 ILE cc_start: 0.8607 (mt) cc_final: 0.8385 (mt) REVERT: B 668 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7120 (ttt-90) REVERT: B 835 ASN cc_start: 0.7859 (m110) cc_final: 0.7488 (t0) outliers start: 62 outliers final: 44 residues processed: 237 average time/residue: 0.2361 time to fit residues: 79.7772 Evaluate side-chains 221 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 3.9990 chunk 113 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.0040 chunk 112 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.207010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.173822 restraints weight = 16516.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.178892 restraints weight = 9476.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.182352 restraints weight = 6528.612| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2410 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= 0.141 Angle : 0.595 10.261 15912 Z= 0.291 Chirality : 0.041 0.136 1876 Planarity : 0.004 0.034 1990 Dihedral : 4.216 18.780 1580 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.31 % Allowed : 33.15 % Favored : 60.54 % 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: -0.99 (0.21), residues: 1446 helix: 0.03 (0.18), residues: 812 sheet: -0.69 (0.42), residues: 140 loop : -1.67 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.006 0.001 HIS A 416 PHE 0.021 0.001 PHE B 146 TYR 0.030 0.002 TYR A 283 ARG 0.005 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 499) hydrogen bonds : angle 4.84377 ( 1422) covalent geometry : bond 0.00333 (11764) covalent geometry : angle 0.59466 (15912) *********************** 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 265 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7255 (tm-30) cc_final: 0.6744 (tt0) REVERT: A 204 GLU cc_start: 0.7283 (mp0) cc_final: 0.6935 (pm20) REVERT: A 226 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7447 (ptp90) REVERT: A 308 LYS cc_start: 0.7401 (ttmm) cc_final: 0.7017 (tttm) REVERT: A 487 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6348 (m-30) REVERT: A 493 ILE cc_start: 0.8608 (mt) cc_final: 0.8371 (mt) REVERT: A 835 ASN cc_start: 0.7912 (m110) cc_final: 0.7484 (t0) REVERT: A 885 MET cc_start: 0.5118 (mmt) cc_final: 0.4836 (mmt) REVERT: A 889 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5939 (pt0) REVERT: B 127 LEU cc_start: 0.8816 (mt) cc_final: 0.8534 (tt) REVERT: B 332 GLU cc_start: 0.6834 (mt-10) cc_final: 0.6452 (tt0) REVERT: B 487 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6548 (m-30) REVERT: B 493 ILE cc_start: 0.8668 (mt) cc_final: 0.8407 (mt) REVERT: B 835 ASN cc_start: 0.7883 (m110) cc_final: 0.7463 (t0) REVERT: B 889 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5961 (pt0) outliers start: 79 outliers final: 52 residues processed: 241 average time/residue: 0.2199 time to fit residues: 77.5355 Evaluate side-chains 236 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 GLN 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 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 724 VAL Chi-restraints excluded: chain A residue 745 ARG Chi-restraints excluded: chain A residue 752 GLN 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 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 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 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 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: 1.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 0.1980 chunk 53 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 476 GLN B 104 GLN ** B 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.205011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.171830 restraints weight = 16484.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.176755 restraints weight = 9578.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.180137 restraints weight = 6677.819| |-----------------------------------------------------------------------------| r_work (final): 0.4336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11764 Z= 0.171 Angle : 0.623 9.761 15912 Z= 0.301 Chirality : 0.042 0.152 1876 Planarity : 0.004 0.036 1990 Dihedral : 4.304 19.035 1580 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.95 % Allowed : 33.07 % Favored : 59.98 % 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: -1.05 (0.21), residues: 1446 helix: -0.05 (0.18), residues: 822 sheet: -0.80 (0.42), residues: 140 loop : -1.61 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 588 HIS 0.007 0.001 HIS A 417 PHE 0.019 0.002 PHE B 146 TYR 0.026 0.002 TYR A 283 ARG 0.004 0.000 ARG B 483 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 499) hydrogen bonds : angle 4.83832 ( 1422) covalent geometry : bond 0.00408 (11764) covalent geometry : angle 0.62265 (15912) *********************** 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 273 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 186 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.5223 (ppp) cc_final: 0.4519 (ppp) REVERT: A 135 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6935 (tt0) REVERT: A 226 ARG cc_start: 0.7804 (ptp90) cc_final: 0.7490 (ptp90) REVERT: A 242 ARG cc_start: 0.7306 (ttp80) cc_final: 0.7050 (ttp80) REVERT: A 308 LYS cc_start: 0.7445 (ttmm) cc_final: 0.6994 (tttm) REVERT: A 463 ILE cc_start: 0.7450 (mm) cc_final: 0.7150 (mm) REVERT: A 487 ASP cc_start: 0.6837 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: A 493 ILE cc_start: 0.8646 (mt) cc_final: 0.8409 (mt) REVERT: A 685 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: A 835 ASN cc_start: 0.7918 (m110) cc_final: 0.7484 (t0) REVERT: A 889 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5982 (pt0) REVERT: B 127 LEU cc_start: 0.8823 (mt) cc_final: 0.8527 (tt) REVERT: B 332 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6516 (tt0) REVERT: B 493 ILE cc_start: 0.8693 (mt) cc_final: 0.8408 (mt) REVERT: B 508 LEU cc_start: 0.8610 (mm) cc_final: 0.8399 (mm) REVERT: B 680 MET cc_start: 0.6642 (tpp) cc_final: 0.6378 (tpp) REVERT: B 685 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 835 ASN cc_start: 0.7872 (m110) cc_final: 0.7456 (t0) REVERT: B 889 GLN cc_start: 0.6203 (OUTLIER) cc_final: 0.5973 (pt0) outliers start: 87 outliers final: 59 residues processed: 250 average time/residue: 0.2148 time to fit residues: 79.2102 Evaluate side-chains 244 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 175 THR 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 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 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 803 ASN Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 831 VAL 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 133 VAL 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 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 619 LEU 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 724 VAL 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 889 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 44 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 140 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 476 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 = 0.4594 r_free = 0.4594 target = 0.207841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.175015 restraints weight = 16574.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180157 restraints weight = 9459.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183636 restraints weight = 6492.679| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11764 Z= 0.112 Angle : 0.582 8.961 15912 Z= 0.281 Chirality : 0.040 0.137 1876 Planarity : 0.004 0.034 1990 Dihedral : 4.163 19.824 1580 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.27 % Allowed : 33.55 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1446 helix: 0.18 (0.18), residues: 814 sheet: -0.76 (0.41), residues: 142 loop : -1.66 (0.26), residues: 490 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 0.018 0.001 PHE B 146 TYR 0.020 0.001 TYR A 283 ARG 0.003 0.000 ARG B 396 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 499) hydrogen bonds : angle 4.62064 ( 1422) covalent geometry : bond 0.00260 (11764) covalent geometry : angle 0.58200 (15912) *********************** 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 248 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6721 (tt0) REVERT: A 142 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7427 (t80) REVERT: A 204 GLU cc_start: 0.7345 (mp0) cc_final: 0.7032 (pm20) REVERT: A 226 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7411 (ptp90) REVERT: A 242 ARG cc_start: 0.7296 (ttp80) cc_final: 0.7095 (ttp80) REVERT: A 308 LYS cc_start: 0.7469 (ttmm) cc_final: 0.7043 (tttm) REVERT: A 487 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6225 (m-30) REVERT: A 493 ILE cc_start: 0.8638 (mt) cc_final: 0.8411 (mt) REVERT: A 685 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: A 835 ASN cc_start: 0.7897 (m110) cc_final: 0.7486 (t0) REVERT: A 885 MET cc_start: 0.5078 (mmt) cc_final: 0.4773 (mmt) REVERT: A 889 GLN cc_start: 0.6233 (OUTLIER) cc_final: 0.6008 (pt0) REVERT: B 127 LEU cc_start: 0.8804 (mt) cc_final: 0.8488 (tt) REVERT: B 142 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7593 (t80) REVERT: B 231 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7182 (tt0) REVERT: B 332 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6415 (tt0) REVERT: B 531 MET cc_start: 0.6654 (tpp) cc_final: 0.6439 (tpt) REVERT: B 685 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 835 ASN cc_start: 0.7856 (m110) cc_final: 0.7455 (t0) REVERT: B 889 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5952 (pt0) outliers start: 66 outliers final: 46 residues processed: 229 average time/residue: 0.2645 time to fit residues: 89.0311 Evaluate side-chains 226 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 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 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 LEU 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 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 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 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 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 422 PHE 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 724 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 0.0980 chunk 87 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4577 r_free = 0.4577 target = 0.206637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.173543 restraints weight = 16714.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.178718 restraints weight = 9529.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.182242 restraints weight = 6531.740| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11764 Z= 0.130 Angle : 0.597 9.311 15912 Z= 0.288 Chirality : 0.041 0.134 1876 Planarity : 0.004 0.035 1990 Dihedral : 4.153 19.127 1580 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 5.67 % Allowed : 33.39 % Favored : 60.94 % 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: -0.88 (0.22), residues: 1446 helix: 0.14 (0.18), residues: 818 sheet: -0.80 (0.41), residues: 142 loop : -1.64 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.007 0.001 HIS A 417 PHE 0.017 0.001 PHE B 146 TYR 0.020 0.001 TYR A 283 ARG 0.003 0.000 ARG B 798 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 499) hydrogen bonds : angle 4.59510 ( 1422) covalent geometry : bond 0.00309 (11764) covalent geometry : angle 0.59719 (15912) *********************** 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 253 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6801 (tt0) REVERT: A 142 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7395 (t80) REVERT: A 226 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7416 (ptp90) REVERT: A 242 ARG cc_start: 0.7306 (ttp80) cc_final: 0.7102 (ttp80) REVERT: A 303 TYR cc_start: 0.6443 (OUTLIER) cc_final: 0.5991 (m-80) REVERT: A 308 LYS cc_start: 0.7526 (ttmm) cc_final: 0.6983 (tttm) REVERT: A 487 ASP cc_start: 0.6747 (OUTLIER) cc_final: 0.6190 (m-30) REVERT: A 493 ILE cc_start: 0.8692 (mt) cc_final: 0.8482 (mt) REVERT: A 685 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 889 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.6011 (pt0) REVERT: B 127 LEU cc_start: 0.8797 (mt) cc_final: 0.8522 (tt) REVERT: B 142 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7618 (t80) REVERT: B 332 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6350 (tt0) REVERT: B 685 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: B 835 ASN cc_start: 0.7897 (m110) cc_final: 0.7490 (t0) REVERT: B 889 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5989 (pt0) outliers start: 71 outliers final: 49 residues processed: 232 average time/residue: 0.2518 time to fit residues: 86.6738 Evaluate side-chains 232 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 175 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 175 THR 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 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 LEU 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 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 810 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 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 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 422 PHE Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 619 LEU 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 724 VAL 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: 0.7980 chunk 94 optimal weight: 0.7980 chunk 79 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 129 optimal weight: 0.0970 chunk 74 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4579 r_free = 0.4579 target = 0.206506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.173754 restraints weight = 16751.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.178881 restraints weight = 9547.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.182404 restraints weight = 6562.203| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11764 Z= 0.132 Angle : 0.613 12.031 15912 Z= 0.294 Chirality : 0.041 0.140 1876 Planarity : 0.004 0.035 1990 Dihedral : 4.163 19.107 1580 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.43 % Favored : 95.37 % Rotamer: Outliers : 5.59 % Allowed : 33.95 % Favored : 60.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.22), residues: 1446 helix: 0.15 (0.18), residues: 818 sheet: -0.66 (0.42), residues: 138 loop : -1.68 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 666 HIS 0.006 0.001 HIS A 417 PHE 0.016 0.001 PHE B 146 TYR 0.019 0.001 TYR A 283 ARG 0.005 0.000 ARG A 798 Details of bonding type rmsd hydrogen bonds : bond 0.03258 ( 499) hydrogen bonds : angle 4.54946 ( 1422) covalent geometry : bond 0.00315 (11764) covalent geometry : angle 0.61339 (15912) *********************** 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 247 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 177 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6822 (tt0) REVERT: A 142 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7304 (t80) REVERT: A 204 GLU cc_start: 0.7334 (mp0) cc_final: 0.7128 (pm20) REVERT: A 226 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7394 (ptp90) REVERT: A 303 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5984 (m-80) REVERT: A 487 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6245 (m-30) REVERT: A 493 ILE cc_start: 0.8700 (mt) cc_final: 0.8490 (mt) REVERT: A 685 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: A 889 GLN cc_start: 0.6192 (OUTLIER) cc_final: 0.5979 (pt0) REVERT: B 127 LEU cc_start: 0.8821 (mt) cc_final: 0.8455 (tt) REVERT: B 142 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7673 (t80) REVERT: B 332 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6395 (tt0) REVERT: B 411 TRP cc_start: 0.3634 (OUTLIER) cc_final: 0.3010 (m-90) REVERT: B 480 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5975 (mtt-85) REVERT: B 493 ILE cc_start: 0.8626 (mt) cc_final: 0.8388 (mt) REVERT: B 685 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: B 835 ASN cc_start: 0.7912 (m110) cc_final: 0.7482 (t0) REVERT: B 889 GLN cc_start: 0.6176 (OUTLIER) cc_final: 0.5961 (pt0) outliers start: 70 outliers final: 57 residues processed: 227 average time/residue: 0.3854 time to fit residues: 133.5171 Evaluate side-chains 239 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 175 THR 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 324 ASP Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 397 LEU 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 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 664 ILE 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 763 THR Chi-restraints excluded: chain A residue 810 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 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 319 VAL 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 480 ARG Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 619 LEU 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 664 ILE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 763 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 62 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 9 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 123 optimal weight: 0.2980 chunk 98 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.4583 r_free = 0.4583 target = 0.207099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.174281 restraints weight = 16657.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.179427 restraints weight = 9509.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.182982 restraints weight = 6533.505| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3006 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= 0.126 Angle : 0.597 9.139 15912 Z= 0.288 Chirality : 0.040 0.134 1876 Planarity : 0.004 0.035 1990 Dihedral : 4.130 19.491 1580 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 5.75 % Allowed : 33.87 % 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 (0.22), residues: 1446 helix: 0.17 (0.18), residues: 818 sheet: -0.69 (0.42), residues: 138 loop : -1.71 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.007 0.001 HIS A 417 PHE 0.015 0.001 PHE B 146 TYR 0.018 0.001 TYR A 283 ARG 0.006 0.000 ARG B 798 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 499) hydrogen bonds : angle 4.49281 ( 1422) covalent geometry : bond 0.00299 (11764) covalent geometry : angle 0.59654 (15912) *********************** 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 248 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6821 (tt0) REVERT: A 142 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7279 (t80) REVERT: A 226 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7381 (ptp90) REVERT: A 303 TYR cc_start: 0.6487 (OUTLIER) cc_final: 0.5876 (m-80) REVERT: A 487 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6221 (m-30) REVERT: A 685 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 127 LEU cc_start: 0.8817 (mt) cc_final: 0.8453 (tt) REVERT: B 142 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7716 (t80) REVERT: B 332 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6362 (tt0) REVERT: B 411 TRP cc_start: 0.3607 (OUTLIER) cc_final: 0.2984 (m-90) REVERT: B 480 ARG cc_start: 0.6327 (OUTLIER) cc_final: 0.5991 (mtt-85) REVERT: B 685 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: B 835 ASN cc_start: 0.7902 (m110) cc_final: 0.7480 (t0) REVERT: B 889 GLN cc_start: 0.6171 (OUTLIER) cc_final: 0.5962 (pt0) outliers start: 72 outliers final: 62 residues processed: 228 average time/residue: 0.3321 time to fit residues: 114.6857 Evaluate side-chains 244 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 173 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 PHE Chi-restraints excluded: chain A residue 175 THR 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 309 LEU Chi-restraints excluded: chain A residue 319 VAL 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 397 LEU 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 535 ILE Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 664 ILE 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 763 THR Chi-restraints excluded: chain A residue 810 LEU 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 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 302 ILE Chi-restraints excluded: chain B residue 319 VAL 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 480 ARG Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 619 LEU 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 664 ILE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain B residue 724 VAL Chi-restraints excluded: chain B residue 744 ASN Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 763 THR 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: 1.9990 chunk 146 optimal weight: 3.9990 chunk 111 optimal weight: 0.0670 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.0000 chunk 123 optimal weight: 0.0970 chunk 121 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 0.3320 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.209148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.176853 restraints weight = 16532.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.182061 restraints weight = 9378.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.185581 restraints weight = 6395.547| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3123 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= 0.109 Angle : 0.602 12.885 15912 Z= 0.288 Chirality : 0.040 0.133 1876 Planarity : 0.004 0.035 1990 Dihedral : 4.034 19.196 1580 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.15 % Favored : 95.71 % Rotamer: Outliers : 5.11 % Allowed : 34.66 % Favored : 60.22 % 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: -0.74 (0.22), residues: 1446 helix: 0.29 (0.18), residues: 818 sheet: -0.49 (0.42), residues: 138 loop : -1.73 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 588 HIS 0.007 0.001 HIS A 417 PHE 0.015 0.001 PHE B 146 TYR 0.016 0.001 TYR A 283 ARG 0.005 0.000 ARG B 798 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 499) hydrogen bonds : angle 4.37729 ( 1422) covalent geometry : bond 0.00254 (11764) covalent geometry : angle 0.60244 (15912) ********************** 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 243 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6806 (tt0) REVERT: A 142 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7167 (t80) REVERT: A 226 ARG cc_start: 0.7639 (ptp90) cc_final: 0.7334 (ptp90) REVERT: A 487 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6120 (m-30) REVERT: A 493 ILE cc_start: 0.8629 (mt) cc_final: 0.8390 (mt) REVERT: A 685 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: A 889 GLN cc_start: 0.6212 (OUTLIER) cc_final: 0.5993 (pt0) REVERT: B 127 LEU cc_start: 0.8789 (mt) cc_final: 0.8438 (tt) REVERT: B 142 PHE cc_start: 0.7944 (OUTLIER) cc_final: 0.7688 (t80) REVERT: B 332 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6242 (tt0) REVERT: B 411 TRP cc_start: 0.3543 (OUTLIER) cc_final: 0.2948 (m-90) REVERT: B 480 ARG cc_start: 0.6206 (OUTLIER) cc_final: 0.5907 (mtt-85) REVERT: B 685 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 835 ASN cc_start: 0.7867 (m110) cc_final: 0.7452 (t0) outliers start: 64 outliers final: 53 residues processed: 223 average time/residue: 0.5042 time to fit residues: 172.0044 Evaluate side-chains 237 residues out of total 1282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 4.419 ------------------------------------------------------------------------------- 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 319 VAL 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 397 LEU 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 619 LEU Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 664 ILE 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 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 319 VAL 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 470 ASP Chi-restraints excluded: chain B residue 480 ARG 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 664 ILE 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 763 THR 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: 0.0370 chunk 75 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 127 optimal weight: 0.4980 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 ** 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 = 0.4600 r_free = 0.4600 target = 0.209086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.176679 restraints weight = 16557.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.181910 restraints weight = 9417.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.185399 restraints weight = 6428.481| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.3184 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= 0.111 Angle : 0.597 10.404 15912 Z= 0.287 Chirality : 0.040 0.174 1876 Planarity : 0.003 0.035 1990 Dihedral : 4.038 19.345 1580 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.56 % Favored : 95.30 % Rotamer: Outliers : 5.27 % Allowed : 34.42 % Favored : 60.30 % 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: -0.70 (0.22), residues: 1446 helix: 0.29 (0.18), residues: 818 sheet: -0.42 (0.40), residues: 152 loop : -1.71 (0.27), residues: 476 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 0.015 0.001 PHE B 146 TYR 0.016 0.001 TYR A 283 ARG 0.005 0.000 ARG B 798 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 499) hydrogen bonds : angle 4.39912 ( 1422) covalent geometry : bond 0.00261 (11764) covalent geometry : angle 0.59689 (15912) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.37 seconds wall clock time: 87 minutes 21.23 seconds (5241.23 seconds total)