Starting phenix.real_space_refine on Fri Feb 14 09:15:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.map" model { file = "/net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ik4_60648/02_2025/9ik4_60648.cif" } resolution = 3.34 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= -0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 64 5.16 5 C 6590 2.51 5 N 1668 2.21 5 O 1778 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10114 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 5016 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 10, 'TRANS': 596} Chain breaks: 2 Chain: "B" Number of atoms: 5016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 5016 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 10, 'TRANS': 596} Chain breaks: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IHP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IHP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.27, per 1000 atoms: 0.62 Number of scatterers: 10114 At special positions: 0 Unit cell: (105.41, 118.69, 95.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 14 15.00 O 1778 8.00 N 1668 7.00 C 6590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 592 " distance=2.03 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 592 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 2 sheets defined 54.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.838A pdb=" N LYS A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 151 removed outlier: 3.765A pdb=" N PHE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP A 113 " --> pdb=" O PHE A 109 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N MET A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 144 " --> pdb=" O GLN A 140 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 317 removed outlier: 4.134A pdb=" N LYS A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 288 " --> pdb=" O HIS A 284 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.798A pdb=" N ILE A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.535A pdb=" N VAL A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.768A pdb=" N TYR A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 403 removed outlier: 3.611A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.646A pdb=" N LEU A 437 " --> pdb=" O MET A 433 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.618A pdb=" N LYS A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.657A pdb=" N ILE A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 490 removed outlier: 3.689A pdb=" N VAL A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.747A pdb=" N LEU A 496 " --> pdb=" O VAL A 492 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 497 " --> pdb=" O HIS A 493 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.516A pdb=" N GLN A 507 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.704A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.521A pdb=" N ARG A 570 " --> pdb=" O PRO A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 595 through 599 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.746A pdb=" N ALA A 614 " --> pdb=" O TYR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 642 removed outlier: 3.698A pdb=" N VAL A 631 " --> pdb=" O THR A 627 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU A 633 " --> pdb=" O HIS A 629 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TYR A 636 " --> pdb=" O ASN A 632 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 639 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.811A pdb=" N ALA A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.627A pdb=" N THR A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 670 " --> pdb=" O SER A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 3.988A pdb=" N PHE A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 711 removed outlier: 3.609A pdb=" N PHE A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 709 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 740 through 748 removed outlier: 3.901A pdb=" N VAL A 745 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 3.643A pdb=" N ASN A 758 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 39 removed outlier: 3.838A pdb=" N LYS B 28 " --> pdb=" O SER B 24 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 151 removed outlier: 3.766A pdb=" N PHE B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N CYS B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP B 113 " --> pdb=" O PHE B 109 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N MET B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 137 " --> pdb=" O ARG B 133 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 144 " --> pdb=" O GLN B 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 146 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 317 removed outlier: 4.134A pdb=" N LYS B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 288 " --> pdb=" O HIS B 284 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B 291 " --> pdb=" O LYS B 287 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU B 295 " --> pdb=" O GLY B 291 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.799A pdb=" N ILE B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 removed outlier: 3.535A pdb=" N VAL B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.501A pdb=" N SER B 345 " --> pdb=" O TYR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.767A pdb=" N TYR B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 403 removed outlier: 3.612A pdb=" N PHE B 393 " --> pdb=" O PHE B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 444 removed outlier: 3.646A pdb=" N LEU B 437 " --> pdb=" O MET B 433 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 442 " --> pdb=" O PHE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.618A pdb=" N LYS B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.658A pdb=" N ILE B 461 " --> pdb=" O ASN B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 483 through 490 removed outlier: 3.689A pdb=" N VAL B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.747A pdb=" N LEU B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 497 " --> pdb=" O HIS B 493 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 499 " --> pdb=" O SER B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 507 removed outlier: 3.515A pdb=" N GLN B 507 " --> pdb=" O PHE B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.703A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 Processing helix chain 'B' and resid 558 through 560 No H-bonds generated for 'chain 'B' and resid 558 through 560' Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.520A pdb=" N ARG B 570 " --> pdb=" O PRO B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 595 through 599 Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.746A pdb=" N ALA B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 642 removed outlier: 3.698A pdb=" N VAL B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU B 633 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR B 636 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 648 removed outlier: 3.811A pdb=" N ALA B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 672 removed outlier: 3.627A pdb=" N THR B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 670 " --> pdb=" O SER B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 removed outlier: 3.988A pdb=" N PHE B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.608A pdb=" N PHE B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET B 709 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 710 " --> pdb=" O TYR B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 740 through 748 removed outlier: 3.902A pdb=" N VAL B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 762 removed outlier: 3.642A pdb=" N ASN B 758 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.815A pdb=" N LYS A 79 " --> pdb=" O VAL A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.816A pdb=" N LYS B 79 " --> pdb=" O VAL B 89 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1576 1.32 - 1.44: 2955 1.44 - 1.56: 5707 1.56 - 1.69: 12 1.69 - 1.81: 106 Bond restraints: 10356 Sorted by residual: bond pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta sigma weight residual 1.459 1.504 -0.045 9.10e-03 1.21e+04 2.45e+01 bond pdb=" O16 IHP B1002 " pdb=" P6 IHP B1002 " ideal model delta sigma weight residual 1.672 1.579 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O16 IHP A 801 " pdb=" P6 IHP A 801 " ideal model delta sigma weight residual 1.672 1.579 0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" N VAL A 430 " pdb=" CA VAL A 430 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.25e-02 6.40e+03 1.62e+01 bond pdb=" O14 IHP B1002 " pdb=" P4 IHP B1002 " ideal model delta sigma weight residual 1.671 1.597 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 10351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 13739 4.48 - 8.97: 213 8.97 - 13.45: 26 13.45 - 17.94: 6 17.94 - 22.42: 2 Bond angle restraints: 13986 Sorted by residual: angle pdb=" N GLY A 412 " pdb=" CA GLY A 412 " pdb=" C GLY A 412 " ideal model delta sigma weight residual 115.36 137.78 -22.42 1.33e+00 5.65e-01 2.84e+02 angle pdb=" N GLY B 412 " pdb=" CA GLY B 412 " pdb=" C GLY B 412 " ideal model delta sigma weight residual 115.36 137.73 -22.37 1.33e+00 5.65e-01 2.83e+02 angle pdb=" N MET B 413 " pdb=" CA MET B 413 " pdb=" C MET B 413 " ideal model delta sigma weight residual 113.88 103.69 10.19 1.23e+00 6.61e-01 6.86e+01 angle pdb=" N MET A 413 " pdb=" CA MET A 413 " pdb=" C MET A 413 " ideal model delta sigma weight residual 113.88 103.71 10.17 1.23e+00 6.61e-01 6.84e+01 angle pdb=" N LEU B 431 " pdb=" CA LEU B 431 " pdb=" C LEU B 431 " ideal model delta sigma weight residual 113.30 102.45 10.85 1.34e+00 5.57e-01 6.55e+01 ... (remaining 13981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.98: 5891 32.98 - 65.95: 241 65.95 - 98.93: 30 98.93 - 131.90: 2 131.90 - 164.88: 6 Dihedral angle restraints: 6170 sinusoidal: 2566 harmonic: 3604 Sorted by residual: dihedral pdb=" CA HIS A 730 " pdb=" C HIS A 730 " pdb=" N VAL A 731 " pdb=" CA VAL A 731 " ideal model delta harmonic sigma weight residual -180.00 -150.70 -29.30 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA HIS B 730 " pdb=" C HIS B 730 " pdb=" N VAL B 731 " pdb=" CA VAL B 731 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLU A 759 " pdb=" C GLU A 759 " pdb=" N HIS A 760 " pdb=" CA HIS A 760 " ideal model delta harmonic sigma weight residual 180.00 152.88 27.12 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 6167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.996: 1520 0.996 - 1.992: 0 1.992 - 2.989: 0 2.989 - 3.985: 0 3.985 - 4.981: 4 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C2 IHP A 801 " pdb=" C1 IHP A 801 " pdb=" C3 IHP A 801 " pdb=" O12 IHP A 801 " both_signs ideal model delta sigma weight residual False -2.52 2.46 -4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C2 IHP B1002 " pdb=" C1 IHP B1002 " pdb=" C3 IHP B1002 " pdb=" O12 IHP B1002 " both_signs ideal model delta sigma weight residual False -2.52 2.46 -4.98 2.00e-01 2.50e+01 6.20e+02 chirality pdb=" C3 IHP B1002 " pdb=" C2 IHP B1002 " pdb=" C4 IHP B1002 " pdb=" O13 IHP B1002 " both_signs ideal model delta sigma weight residual False -2.34 2.46 -4.79 2.00e-01 2.50e+01 5.75e+02 ... (remaining 1521 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 428 " 0.075 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 429 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 671 " -0.029 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR B 671 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 671 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR B 671 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 671 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 671 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 671 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 671 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 671 " 0.028 2.00e-02 2.50e+03 2.57e-02 1.32e+01 pdb=" CG TYR A 671 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR A 671 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 671 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 671 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 671 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 671 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 671 " -0.000 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 77 2.48 - 3.09: 6250 3.09 - 3.69: 15588 3.69 - 4.30: 21985 4.30 - 4.90: 35392 Nonbonded interactions: 79292 Sorted by model distance: nonbonded pdb=" CD2 TYR A 733 " pdb=" CG2 THR A 736 " model vdw 1.881 3.760 nonbonded pdb=" CD2 TYR B 733 " pdb=" CG2 THR B 736 " model vdw 1.882 3.760 nonbonded pdb=" CE2 TYR A 733 " pdb=" CG2 THR A 736 " model vdw 1.982 3.760 nonbonded pdb=" CE2 TYR B 733 " pdb=" CG2 THR B 736 " model vdw 1.985 3.760 nonbonded pdb=" O GLN B 587 " pdb=" OD1 ASP B 588 " model vdw 2.018 3.040 ... (remaining 79287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 772) selection = (chain 'B' and resid 11 through 772) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.960 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 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 : 0.008 0.093 10356 Z= 0.537 Angle : 1.414 22.423 13986 Z= 0.796 Chirality : 0.257 4.981 1524 Planarity : 0.007 0.115 1702 Dihedral : 19.372 164.880 3844 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.06 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Cbeta Deviations : 0.09 % 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: -6.52 (0.15), residues: 1202 helix: -4.31 (0.10), residues: 746 sheet: -2.30 (0.99), residues: 24 loop : -4.15 (0.23), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 657 HIS 0.016 0.002 HIS B 284 PHE 0.048 0.004 PHE B 20 TYR 0.063 0.003 TYR B 671 ARG 0.015 0.001 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 VAL cc_start: 0.6120 (t) cc_final: 0.5881 (m) REVERT: B 335 LYS cc_start: 0.6748 (mmpt) cc_final: 0.6214 (ptmt) REVERT: B 410 LEU cc_start: 0.7367 (tt) cc_final: 0.6683 (mt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2347 time to fit residues: 66.7403 Evaluate side-chains 162 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.0570 chunk 94 optimal weight: 0.0770 chunk 36 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 108 optimal weight: 0.0770 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 120 ASN A 157 ASN A 284 HIS ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 ASN A 629 HIS B 11 GLN B 120 ASN B 157 ASN B 284 HIS B 301 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5043 r_free = 0.5043 target = 0.277291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.237850 restraints weight = 10779.324| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.01 r_work: 0.4194 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10356 Z= 0.170 Angle : 0.804 13.355 13986 Z= 0.405 Chirality : 0.052 0.647 1524 Planarity : 0.005 0.070 1702 Dihedral : 13.414 98.424 1424 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 2.22 % Allowed : 17.13 % Favored : 80.65 % 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: -5.30 (0.19), residues: 1202 helix: -3.19 (0.15), residues: 752 sheet: -2.18 (1.01), residues: 24 loop : -3.97 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 612 HIS 0.015 0.002 HIS A 384 PHE 0.029 0.001 PHE B 622 TYR 0.024 0.002 TYR B 671 ARG 0.003 0.001 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 VAL cc_start: 0.3289 (OUTLIER) cc_final: 0.3004 (m) REVERT: A 335 LYS cc_start: 0.7487 (mmmt) cc_final: 0.6254 (ptmt) REVERT: A 349 MET cc_start: 0.7448 (mmt) cc_final: 0.7033 (mmm) REVERT: A 410 LEU cc_start: 0.7147 (tt) cc_final: 0.6426 (mt) REVERT: A 569 LEU cc_start: 0.7924 (mt) cc_final: 0.7721 (mt) REVERT: B 89 VAL cc_start: 0.3339 (OUTLIER) cc_final: 0.3058 (m) REVERT: B 335 LYS cc_start: 0.7643 (mmpt) cc_final: 0.6251 (ptmt) REVERT: B 410 LEU cc_start: 0.7301 (tt) cc_final: 0.6511 (mt) REVERT: B 569 LEU cc_start: 0.7995 (mt) cc_final: 0.7779 (mt) REVERT: B 590 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7086 (mm-30) outliers start: 24 outliers final: 12 residues processed: 173 average time/residue: 0.2191 time to fit residues: 53.9668 Evaluate side-chains 155 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 316 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 587 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.269513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.223441 restraints weight = 10980.468| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 3.33 r_work: 0.4060 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10356 Z= 0.344 Angle : 0.798 10.493 13986 Z= 0.411 Chirality : 0.049 0.374 1524 Planarity : 0.005 0.053 1702 Dihedral : 13.063 93.685 1424 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 3.70 % Allowed : 18.89 % Favored : 77.41 % 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: -4.95 (0.20), residues: 1202 helix: -2.84 (0.16), residues: 772 sheet: -2.00 (1.00), residues: 24 loop : -3.99 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 621 HIS 0.013 0.001 HIS B 384 PHE 0.021 0.002 PHE A 728 TYR 0.026 0.002 TYR B 671 ARG 0.006 0.001 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 335 LYS cc_start: 0.7500 (mmmt) cc_final: 0.6279 (ptmt) REVERT: A 349 MET cc_start: 0.7657 (mmt) cc_final: 0.7192 (mmm) REVERT: A 410 LEU cc_start: 0.7337 (tt) cc_final: 0.6570 (mt) REVERT: B 335 LYS cc_start: 0.7710 (mmpt) cc_final: 0.6275 (ptmt) outliers start: 40 outliers final: 26 residues processed: 175 average time/residue: 0.2072 time to fit residues: 52.1537 Evaluate side-chains 168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 53 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 316 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5010 r_free = 0.5010 target = 0.273187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.229466 restraints weight = 10774.633| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 2.97 r_work: 0.4137 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10356 Z= 0.205 Angle : 0.697 11.994 13986 Z= 0.358 Chirality : 0.042 0.231 1524 Planarity : 0.004 0.045 1702 Dihedral : 12.611 89.659 1424 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 3.89 % Allowed : 20.74 % Favored : 75.37 % 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: -4.49 (0.21), residues: 1202 helix: -2.49 (0.17), residues: 778 sheet: -1.77 (1.01), residues: 24 loop : -3.79 (0.27), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 751 HIS 0.007 0.001 HIS B 384 PHE 0.016 0.001 PHE A 122 TYR 0.021 0.002 TYR B 306 ARG 0.004 0.000 ARG B 473 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 144 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 132 GLU cc_start: 0.8576 (tp30) cc_final: 0.8153 (tp30) REVERT: A 335 LYS cc_start: 0.7447 (mmmt) cc_final: 0.6407 (ptmt) REVERT: A 349 MET cc_start: 0.7686 (mmt) cc_final: 0.7338 (mmm) REVERT: A 503 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.5956 (t80) REVERT: A 756 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6221 (mm) REVERT: B 25 GLN cc_start: 0.6833 (tm130) cc_final: 0.6298 (tp40) REVERT: B 335 LYS cc_start: 0.7643 (mmpt) cc_final: 0.6352 (ptmt) REVERT: B 503 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6329 (t80) REVERT: B 756 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6216 (mm) outliers start: 42 outliers final: 24 residues processed: 171 average time/residue: 0.2104 time to fit residues: 51.8011 Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 503 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 593 MET Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 301 ASN A 343 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS B 117 ASN B 301 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4995 r_free = 0.4995 target = 0.271164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.229101 restraints weight = 10870.735| |-----------------------------------------------------------------------------| r_work (start): 0.4641 rms_B_bonded: 2.98 r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10356 Z= 0.249 Angle : 0.720 11.227 13986 Z= 0.365 Chirality : 0.043 0.187 1524 Planarity : 0.004 0.044 1702 Dihedral : 12.323 86.543 1424 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 5.28 % Allowed : 20.19 % Favored : 74.54 % 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: -4.33 (0.22), residues: 1202 helix: -2.34 (0.17), residues: 768 sheet: -2.15 (0.93), residues: 28 loop : -3.75 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 675 HIS 0.007 0.001 HIS B 384 PHE 0.017 0.002 PHE A 728 TYR 0.021 0.002 TYR B 472 ARG 0.005 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.049 Fit side-chains revert: symmetry clash REVERT: A 25 GLN cc_start: 0.5798 (tm130) cc_final: 0.5597 (tp40) REVERT: A 503 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5861 (t80) REVERT: A 756 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5646 (mm) REVERT: B 25 GLN cc_start: 0.5732 (tm130) cc_final: 0.5531 (tp40) REVERT: B 335 LYS cc_start: 0.6812 (mmpt) cc_final: 0.6299 (ptmt) REVERT: B 433 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7279 (ttt) REVERT: B 756 LEU cc_start: 0.5982 (OUTLIER) cc_final: 0.5671 (mm) outliers start: 57 outliers final: 34 residues processed: 176 average time/residue: 0.1915 time to fit residues: 50.0507 Evaluate side-chains 168 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 738 LEU Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 35 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 91 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 38 optimal weight: 0.0270 chunk 98 optimal weight: 0.0040 chunk 97 optimal weight: 0.9990 overall best weight: 0.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 343 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5034 r_free = 0.5034 target = 0.276583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.232193 restraints weight = 10893.784| |-----------------------------------------------------------------------------| r_work (start): 0.4658 rms_B_bonded: 3.02 r_work: 0.4162 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10356 Z= 0.149 Angle : 0.686 12.235 13986 Z= 0.343 Chirality : 0.040 0.177 1524 Planarity : 0.003 0.041 1702 Dihedral : 12.072 84.838 1424 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 3.61 % Allowed : 22.59 % Favored : 73.80 % 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: -4.08 (0.22), residues: 1202 helix: -2.13 (0.18), residues: 754 sheet: -1.96 (0.95), residues: 28 loop : -3.66 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 675 HIS 0.006 0.001 HIS B 384 PHE 0.010 0.001 PHE B 422 TYR 0.021 0.001 TYR B 306 ARG 0.006 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.155 Fit side-chains REVERT: A 25 GLN cc_start: 0.6825 (tm130) cc_final: 0.6409 (tp40) REVERT: A 503 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6342 (t80) REVERT: A 569 LEU cc_start: 0.8003 (mt) cc_final: 0.7766 (mt) REVERT: A 636 TYR cc_start: 0.8212 (m-80) cc_final: 0.7608 (m-80) REVERT: B 25 GLN cc_start: 0.6804 (tm130) cc_final: 0.6320 (tp40) REVERT: B 569 LEU cc_start: 0.8036 (mt) cc_final: 0.7794 (mt) REVERT: B 636 TYR cc_start: 0.8192 (m-80) cc_final: 0.7488 (m-80) outliers start: 39 outliers final: 22 residues processed: 170 average time/residue: 0.2023 time to fit residues: 50.3056 Evaluate side-chains 156 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 503 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 362 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.271634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.228752 restraints weight = 10980.817| |-----------------------------------------------------------------------------| r_work (start): 0.4633 rms_B_bonded: 3.39 r_work (final): 0.4633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10356 Z= 0.272 Angle : 0.734 11.042 13986 Z= 0.367 Chirality : 0.043 0.192 1524 Planarity : 0.004 0.042 1702 Dihedral : 11.884 81.637 1424 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 4.35 % Allowed : 22.59 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.02 (0.23), residues: 1202 helix: -2.10 (0.18), residues: 772 sheet: -1.76 (0.97), residues: 28 loop : -3.66 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 675 HIS 0.005 0.001 HIS A 384 PHE 0.017 0.002 PHE A 767 TYR 0.018 0.002 TYR B 472 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 129 time to evaluate : 1.169 Fit side-chains REVERT: A 756 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5717 (mm) REVERT: B 25 GLN cc_start: 0.5899 (tm130) cc_final: 0.5672 (tp40) REVERT: B 756 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5723 (mm) outliers start: 47 outliers final: 35 residues processed: 160 average time/residue: 0.1901 time to fit residues: 45.1417 Evaluate side-chains 166 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 301 ASN Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 343 ASN A 384 HIS ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.272771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.226888 restraints weight = 10948.384| |-----------------------------------------------------------------------------| r_work (start): 0.4615 rms_B_bonded: 3.17 r_work: 0.4092 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10356 Z= 0.222 Angle : 0.732 11.040 13986 Z= 0.359 Chirality : 0.042 0.190 1524 Planarity : 0.003 0.044 1702 Dihedral : 11.419 78.110 1424 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 3.70 % Allowed : 23.52 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.22), residues: 1202 helix: -2.05 (0.18), residues: 782 sheet: -1.74 (0.96), residues: 28 loop : -3.69 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 675 HIS 0.005 0.001 HIS A 384 PHE 0.014 0.001 PHE A 767 TYR 0.021 0.002 TYR B 341 ARG 0.003 0.000 ARG A 473 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.100 Fit side-chains REVERT: A 756 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6281 (mm) REVERT: B 25 GLN cc_start: 0.6855 (tm130) cc_final: 0.6320 (tp40) REVERT: B 433 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7408 (ttt) REVERT: B 756 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6313 (mm) outliers start: 40 outliers final: 34 residues processed: 159 average time/residue: 0.2008 time to fit residues: 47.5569 Evaluate side-chains 165 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 578 TYR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 86 optimal weight: 0.0570 chunk 56 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.265301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.219041 restraints weight = 10962.022| |-----------------------------------------------------------------------------| r_work (start): 0.4553 rms_B_bonded: 3.09 r_work: 0.4018 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 10356 Z= 0.461 Angle : 0.862 10.042 13986 Z= 0.432 Chirality : 0.049 0.200 1524 Planarity : 0.005 0.050 1702 Dihedral : 10.797 69.288 1424 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.39 % Favored : 86.61 % Rotamer: Outliers : 3.89 % Allowed : 24.44 % Favored : 71.67 % 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: -4.21 (0.22), residues: 1202 helix: -2.23 (0.17), residues: 790 sheet: -1.75 (0.96), residues: 28 loop : -3.84 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 675 HIS 0.006 0.001 HIS A 384 PHE 0.028 0.002 PHE A 767 TYR 0.019 0.002 TYR B 671 ARG 0.003 0.001 ARG B 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 134 time to evaluate : 1.068 Fit side-chains REVERT: A 756 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6436 (mm) REVERT: B 25 GLN cc_start: 0.6883 (tm130) cc_final: 0.6352 (tp40) REVERT: B 335 LYS cc_start: 0.7595 (mmpt) cc_final: 0.6362 (ptmt) REVERT: B 433 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7590 (ttt) REVERT: B 756 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6440 (mm) outliers start: 42 outliers final: 30 residues processed: 163 average time/residue: 0.2000 time to fit residues: 47.7177 Evaluate side-chains 164 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 433 MET Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 756 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 0.0070 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.0670 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 343 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 616 GLN ** A 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 ASN B 120 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.274511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.228606 restraints weight = 10873.791| |-----------------------------------------------------------------------------| r_work (start): 0.4632 rms_B_bonded: 2.81 r_work: 0.4145 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.159 Angle : 0.739 11.298 13986 Z= 0.360 Chirality : 0.041 0.245 1524 Planarity : 0.003 0.049 1702 Dihedral : 9.979 64.977 1424 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 1.57 % Allowed : 27.50 % Favored : 70.93 % 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: -3.87 (0.23), residues: 1202 helix: -1.97 (0.18), residues: 784 sheet: -1.68 (0.97), residues: 28 loop : -3.66 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 675 HIS 0.007 0.001 HIS B 384 PHE 0.011 0.001 PHE B 677 TYR 0.024 0.001 TYR B 472 ARG 0.005 0.000 ARG A 473 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2404 Ramachandran restraints generated. 1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.171 Fit side-chains REVERT: A 301 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.7552 (m-40) REVERT: A 553 MET cc_start: 0.8356 (tpp) cc_final: 0.8129 (tpp) REVERT: B 25 GLN cc_start: 0.6871 (tm130) cc_final: 0.6342 (tp40) REVERT: B 335 LYS cc_start: 0.7534 (mmpt) cc_final: 0.6456 (ptmt) REVERT: B 553 MET cc_start: 0.8374 (tpp) cc_final: 0.8091 (tpp) outliers start: 17 outliers final: 14 residues processed: 149 average time/residue: 0.2089 time to fit residues: 45.3467 Evaluate side-chains 146 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 546 SER Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 588 ASP Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 770 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 120 ASN ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 384 HIS ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 725 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.272947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.229126 restraints weight = 10620.766| |-----------------------------------------------------------------------------| r_work (start): 0.4646 rms_B_bonded: 2.95 r_work: 0.4106 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10356 Z= 0.326 Angle : 0.796 10.399 13986 Z= 0.395 Chirality : 0.046 0.231 1524 Planarity : 0.004 0.046 1702 Dihedral : 9.636 57.976 1424 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.06 % Favored : 86.94 % Rotamer: Outliers : 1.85 % Allowed : 26.85 % Favored : 71.30 % 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: -3.95 (0.23), residues: 1202 helix: -2.00 (0.18), residues: 792 sheet: -1.63 (0.98), residues: 28 loop : -3.81 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 675 HIS 0.006 0.001 HIS A 384 PHE 0.022 0.002 PHE A 767 TYR 0.024 0.002 TYR B 472 ARG 0.003 0.000 ARG A 748 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4833.48 seconds wall clock time: 86 minutes 36.03 seconds (5196.03 seconds total)