Starting phenix.real_space_refine on Thu May 1 01:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0i_39704/05_2025/8z0i_39704.cif" } resolution = 3.45 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 68 5.16 5 C 6470 2.51 5 N 1664 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10004 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4970 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 25, 'TRANS': 608} Chain breaks: 1 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 4970 Classifications: {'peptide': 634} Link IDs: {'PTRANS': 25, 'TRANS': 608} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.49, per 1000 atoms: 0.65 Number of scatterers: 10004 At special positions: 0 Unit cell: (85.92, 74.106, 152.508, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 68 16.00 P 6 15.00 Mg 2 11.99 O 1794 8.00 N 1664 7.00 C 6470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 568 " 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=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 10 sheets defined 49.3% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.719A pdb=" N PHE A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.704A pdb=" N PHE A 169 " --> pdb=" O GLY A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.186A pdb=" N ASN A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.511A pdb=" N SER A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 4.134A pdb=" N SER A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 4.025A pdb=" N GLN A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 removed outlier: 4.101A pdb=" N ARG A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN A 264 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 265 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.858A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.743A pdb=" N PHE A 426 " --> pdb=" O GLN A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 Processing helix chain 'A' and resid 487 through 496 removed outlier: 3.674A pdb=" N VAL A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 522 through 524 No H-bonds generated for 'chain 'A' and resid 522 through 524' Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 544 through 554 removed outlier: 3.777A pdb=" N ILE A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 566 removed outlier: 3.533A pdb=" N GLN A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 564 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.642A pdb=" N PHE A 596 " --> pdb=" O SER A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.559A pdb=" N PHE A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 665 removed outlier: 3.868A pdb=" N ILE A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 641 " --> pdb=" O PRO A 637 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLN A 648 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 700 removed outlier: 3.742A pdb=" N VAL A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 696 " --> pdb=" O PHE A 692 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.824A pdb=" N ILE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 731 through 739 removed outlier: 3.618A pdb=" N THR A 739 " --> pdb=" O ARG A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.573A pdb=" N THR A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 789 removed outlier: 4.103A pdb=" N PHE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TRP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 782 " --> pdb=" O ALA A 778 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 783 " --> pdb=" O PHE A 779 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 157 through 165 removed outlier: 4.043A pdb=" N MET B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 removed outlier: 3.781A pdb=" N PHE B 169 " --> pdb=" O GLY B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.253A pdb=" N ASN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.948A pdb=" N ALA B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 259 through 265 removed outlier: 3.647A pdb=" N ARG B 263 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 264 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.718A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.762A pdb=" N PHE B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.790A pdb=" N PHE B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 removed outlier: 3.592A pdb=" N LEU B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.571A pdb=" N VAL B 492 " --> pdb=" O PRO B 488 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.678A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.661A pdb=" N GLN B 531 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 554 removed outlier: 4.039A pdb=" N ILE B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLN B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 566 removed outlier: 3.565A pdb=" N GLN B 558 " --> pdb=" O GLN B 554 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.584A pdb=" N PHE B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.995A pdb=" N LEU B 603 " --> pdb=" O PRO B 599 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.099A pdb=" N VAL B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 665 removed outlier: 3.687A pdb=" N ILE B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 641 " --> pdb=" O PRO B 637 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 654 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 700 removed outlier: 4.048A pdb=" N VAL B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 686 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 694 " --> pdb=" O MET B 690 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 696 " --> pdb=" O PHE B 692 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 711 removed outlier: 3.570A pdb=" N ILE B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLN B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU B 709 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 714 No H-bonds generated for 'chain 'B' and resid 712 through 714' Processing helix chain 'B' and resid 715 through 720 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 745 through 755 removed outlier: 3.619A pdb=" N THR B 755 " --> pdb=" O ARG B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 790 removed outlier: 3.589A pdb=" N TYR B 766 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR B 767 " --> pdb=" O PRO B 763 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLY B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N PHE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 783 " --> pdb=" O PHE B 779 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.584A pdb=" N MET A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL A 64 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.658A pdb=" N TYR A 96 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 95 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY A 269 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 97 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N MET A 271 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 99 " --> pdb=" O MET A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 535 removed outlier: 5.737A pdb=" N VAL A 534 " --> pdb=" O SER B 580 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.503A pdb=" N SER A 580 " --> pdb=" O VAL B 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.566A pdb=" N MET B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 64 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.550A pdb=" N LEU B 99 " --> pdb=" O MET B 271 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 270 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 437 through 441 Processing sheet with id=AB1, first strand: chain 'B' and resid 502 through 503 307 hydrogen bonds defined for protein. 888 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: 2.47 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2989 1.33 - 1.45: 1482 1.45 - 1.57: 5640 1.57 - 1.69: 9 1.69 - 1.81: 108 Bond restraints: 10228 Sorted by residual: bond pdb=" CB GLN B 543 " pdb=" CG GLN B 543 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.09e+00 bond pdb=" N GLU A 295 " pdb=" CA GLU A 295 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N GLU B 295 " pdb=" CA GLU B 295 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.65e+00 bond pdb=" N ASN B 450 " pdb=" CA ASN B 450 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.35e+00 bond pdb=" CB PRO B 637 " pdb=" CG PRO B 637 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.12e+00 ... (remaining 10223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 13686 2.04 - 4.09: 172 4.09 - 6.13: 20 6.13 - 8.18: 8 8.18 - 10.22: 4 Bond angle restraints: 13890 Sorted by residual: angle pdb=" CA GLN B 543 " pdb=" CB GLN B 543 " pdb=" CG GLN B 543 " ideal model delta sigma weight residual 114.10 123.81 -9.71 2.00e+00 2.50e-01 2.36e+01 angle pdb=" CB GLN B 543 " pdb=" CG GLN B 543 " pdb=" CD GLN B 543 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" CA PRO B 637 " pdb=" N PRO B 637 " pdb=" CD PRO B 637 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" N VAL B 423 " pdb=" CA VAL B 423 " pdb=" C VAL B 423 " ideal model delta sigma weight residual 111.81 109.05 2.76 8.60e-01 1.35e+00 1.03e+01 angle pdb=" N VAL A 423 " pdb=" CA VAL A 423 " pdb=" C VAL A 423 " ideal model delta sigma weight residual 111.81 109.06 2.75 8.60e-01 1.35e+00 1.02e+01 ... (remaining 13885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4971 17.59 - 35.17: 783 35.17 - 52.76: 261 52.76 - 70.34: 49 70.34 - 87.93: 16 Dihedral angle restraints: 6080 sinusoidal: 2446 harmonic: 3634 Sorted by residual: dihedral pdb=" CB CYS B 462 " pdb=" SG CYS B 462 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual 93.00 145.26 -52.26 1 1.00e+01 1.00e-02 3.72e+01 dihedral pdb=" CA VAL B 196 " pdb=" C VAL B 196 " pdb=" N LYS B 197 " pdb=" CA LYS B 197 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA TRP A 167 " pdb=" C TRP A 167 " pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 6077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1092 0.040 - 0.080: 403 0.080 - 0.120: 91 0.120 - 0.160: 6 0.160 - 0.200: 2 Chirality restraints: 1594 Sorted by residual: chirality pdb=" CA GLN B 543 " pdb=" N GLN B 543 " pdb=" C GLN B 543 " pdb=" CB GLN B 543 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA PRO B 637 " pdb=" N PRO B 637 " pdb=" C PRO B 637 " pdb=" CB PRO B 637 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB ILE A 124 " pdb=" CA ILE A 124 " pdb=" CG1 ILE A 124 " pdb=" CG2 ILE A 124 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1591 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 636 " 0.064 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO B 637 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 637 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 637 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 294 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C LEU B 294 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU B 294 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 295 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 577 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO B 578 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 578 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 578 " 0.022 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 366 2.72 - 3.26: 9791 3.26 - 3.81: 14795 3.81 - 4.35: 18599 4.35 - 4.90: 32567 Nonbonded interactions: 76118 Sorted by model distance: nonbonded pdb=" OG1 THR A 636 " pdb=" OE2 GLU A 639 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 200 " pdb=" OE1 GLN A 203 " model vdw 2.177 3.040 nonbonded pdb=" NZ LYS A 446 " pdb=" O GLU A 455 " model vdw 2.193 3.120 nonbonded pdb=" O SER A 615 " pdb=" OG SER A 697 " model vdw 2.197 3.040 nonbonded pdb=" OG SER B 200 " pdb=" OE1 GLN B 203 " model vdw 2.226 3.040 ... (remaining 76113 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 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: 3.860 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: 0.060 Set scattering table: 0.080 Process input model: 23.970 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10230 Z= 0.155 Angle : 0.612 10.221 13894 Z= 0.309 Chirality : 0.042 0.200 1594 Planarity : 0.004 0.094 1728 Dihedral : 19.113 87.930 3746 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.74 % Allowed : 36.25 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.06 (0.22), residues: 1260 helix: -2.11 (0.19), residues: 600 sheet: -1.88 (0.52), residues: 104 loop : -1.79 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 125 HIS 0.003 0.001 HIS A 266 PHE 0.008 0.001 PHE A 607 TYR 0.013 0.001 TYR A 766 ARG 0.001 0.000 ARG B 116 Details of bonding type rmsd hydrogen bonds : bond 0.28204 ( 307) hydrogen bonds : angle 8.43280 ( 888) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.34868 ( 4) covalent geometry : bond 0.00375 (10228) covalent geometry : angle 0.61223 (13890) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 1.057 Fit side-chains REVERT: A 714 PHE cc_start: 0.6413 (m-10) cc_final: 0.5937 (m-10) outliers start: 8 outliers final: 4 residues processed: 145 average time/residue: 0.2548 time to fit residues: 50.8752 Evaluate side-chains 143 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 474 ASN A 497 GLN A 708 GLN B 499 HIS B 542 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.102744 restraints weight = 13809.704| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.55 r_work: 0.2962 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10230 Z= 0.155 Angle : 0.592 10.380 13894 Z= 0.300 Chirality : 0.043 0.213 1594 Planarity : 0.004 0.040 1728 Dihedral : 8.031 81.253 1435 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 5.26 % Allowed : 32.38 % Favored : 62.36 % 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: -2.71 (0.23), residues: 1260 helix: -1.60 (0.20), residues: 606 sheet: -2.37 (0.57), residues: 80 loop : -1.81 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 125 HIS 0.003 0.001 HIS B 257 PHE 0.011 0.001 PHE A 607 TYR 0.017 0.001 TYR A 736 ARG 0.001 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 307) hydrogen bonds : angle 5.06805 ( 888) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.36231 ( 4) covalent geometry : bond 0.00378 (10228) covalent geometry : angle 0.59222 (13890) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 1.085 Fit side-chains REVERT: A 398 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8273 (tt) REVERT: A 444 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7552 (m-70) REVERT: A 474 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8145 (t0) REVERT: A 704 ARG cc_start: 0.7664 (mtp85) cc_final: 0.7334 (mtp-110) REVERT: A 709 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8266 (tt) REVERT: B 168 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8304 (mt) REVERT: B 444 HIS cc_start: 0.8356 (OUTLIER) cc_final: 0.7711 (m170) REVERT: B 639 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7324 (mt-10) outliers start: 57 outliers final: 31 residues processed: 185 average time/residue: 0.2203 time to fit residues: 57.0935 Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 125 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102789 restraints weight = 13922.298| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.55 r_work: 0.3002 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10230 Z= 0.130 Angle : 0.587 15.430 13894 Z= 0.289 Chirality : 0.042 0.223 1594 Planarity : 0.004 0.039 1728 Dihedral : 7.193 77.961 1430 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.17 % Allowed : 32.56 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.52 (0.23), residues: 1260 helix: -1.37 (0.21), residues: 610 sheet: -2.32 (0.57), residues: 80 loop : -1.80 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 125 HIS 0.003 0.001 HIS A 444 PHE 0.011 0.001 PHE A 607 TYR 0.013 0.001 TYR A 736 ARG 0.002 0.000 ARG B 535 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 307) hydrogen bonds : angle 4.57109 ( 888) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.29656 ( 4) covalent geometry : bond 0.00314 (10228) covalent geometry : angle 0.58691 (13890) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 1.123 Fit side-chains REVERT: A 398 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 474 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8173 (t0) REVERT: A 563 ASP cc_start: 0.7760 (t0) cc_final: 0.7383 (t0) REVERT: A 704 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7297 (mtp-110) REVERT: A 709 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 168 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B 444 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.7818 (m170) outliers start: 56 outliers final: 30 residues processed: 180 average time/residue: 0.2295 time to fit residues: 57.8052 Evaluate side-chains 161 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 690 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 25 optimal weight: 0.0030 chunk 123 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 33 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN B 497 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.105089 restraints weight = 13693.516| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.53 r_work: 0.3048 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10230 Z= 0.102 Angle : 0.563 13.677 13894 Z= 0.274 Chirality : 0.041 0.225 1594 Planarity : 0.003 0.038 1728 Dihedral : 6.693 74.235 1430 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.89 % Allowed : 33.39 % Favored : 61.72 % 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: -2.31 (0.23), residues: 1260 helix: -1.10 (0.22), residues: 600 sheet: -2.26 (0.58), residues: 80 loop : -1.81 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 125 HIS 0.002 0.001 HIS A 240 PHE 0.010 0.001 PHE A 607 TYR 0.011 0.001 TYR A 736 ARG 0.002 0.000 ARG B 535 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 307) hydrogen bonds : angle 4.24834 ( 888) SS BOND : bond 0.00048 ( 2) SS BOND : angle 0.25506 ( 4) covalent geometry : bond 0.00239 (10228) covalent geometry : angle 0.56263 (13890) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 140 time to evaluate : 1.079 Fit side-chains REVERT: A 398 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8108 (tt) REVERT: A 563 ASP cc_start: 0.7748 (t0) cc_final: 0.7399 (t0) REVERT: A 687 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7590 (tt) REVERT: A 709 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8149 (tt) REVERT: B 168 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8005 (mt) REVERT: B 444 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7711 (m170) REVERT: B 460 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7642 (t80) REVERT: B 543 GLN cc_start: 0.8114 (mp10) cc_final: 0.7249 (mp10) outliers start: 53 outliers final: 29 residues processed: 185 average time/residue: 0.2303 time to fit residues: 59.5233 Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 264 GLN Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 218 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 690 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.102076 restraints weight = 13812.939| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.55 r_work: 0.2990 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10230 Z= 0.152 Angle : 0.600 13.365 13894 Z= 0.293 Chirality : 0.043 0.232 1594 Planarity : 0.004 0.040 1728 Dihedral : 6.497 78.336 1430 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 5.72 % Allowed : 33.39 % Favored : 60.89 % 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: -2.31 (0.23), residues: 1260 helix: -1.10 (0.22), residues: 596 sheet: -2.08 (0.60), residues: 74 loop : -1.85 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 125 HIS 0.003 0.001 HIS A 444 PHE 0.013 0.001 PHE A 607 TYR 0.012 0.001 TYR A 766 ARG 0.002 0.000 ARG B 535 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 307) hydrogen bonds : angle 4.28604 ( 888) SS BOND : bond 0.00091 ( 2) SS BOND : angle 0.30936 ( 4) covalent geometry : bond 0.00372 (10228) covalent geometry : angle 0.59973 (13890) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 128 time to evaluate : 1.203 Fit side-chains REVERT: A 272 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.5643 (tpp-160) REVERT: A 398 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 530 ASP cc_start: 0.8036 (t70) cc_final: 0.7826 (t70) REVERT: A 563 ASP cc_start: 0.7888 (t0) cc_final: 0.7567 (t0) REVERT: A 687 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7753 (tt) REVERT: A 709 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8239 (tt) REVERT: B 168 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8369 (mt) REVERT: B 444 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.7819 (m170) REVERT: B 460 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7631 (t80) REVERT: B 687 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7701 (tt) REVERT: B 735 ARG cc_start: 0.8546 (ttm170) cc_final: 0.8223 (ttp-170) outliers start: 62 outliers final: 44 residues processed: 180 average time/residue: 0.2221 time to fit residues: 56.4794 Evaluate side-chains 177 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 125 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN A 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096789 restraints weight = 14155.727| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.59 r_work: 0.2893 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10230 Z= 0.274 Angle : 0.701 13.764 13894 Z= 0.350 Chirality : 0.047 0.178 1594 Planarity : 0.004 0.045 1728 Dihedral : 6.865 89.217 1430 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 7.29 % Allowed : 31.64 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.57 (0.23), residues: 1260 helix: -1.33 (0.21), residues: 594 sheet: -2.25 (0.58), residues: 74 loop : -1.96 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 631 HIS 0.005 0.001 HIS A 266 PHE 0.018 0.002 PHE A 607 TYR 0.015 0.002 TYR A 766 ARG 0.002 0.000 ARG A 704 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 307) hydrogen bonds : angle 4.72465 ( 888) SS BOND : bond 0.00194 ( 2) SS BOND : angle 0.47934 ( 4) covalent geometry : bond 0.00678 (10228) covalent geometry : angle 0.70090 (13890) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 119 time to evaluate : 1.105 Fit side-chains REVERT: A 168 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 272 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.5780 (tpp-160) REVERT: A 444 HIS cc_start: 0.8262 (OUTLIER) cc_final: 0.7441 (m-70) REVERT: A 563 ASP cc_start: 0.7941 (t0) cc_final: 0.7649 (t0) REVERT: A 687 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 704 ARG cc_start: 0.7569 (mtp85) cc_final: 0.7064 (mtm110) REVERT: A 709 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8252 (tt) REVERT: B 119 LEU cc_start: 0.8748 (tp) cc_final: 0.8438 (tt) REVERT: B 168 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 172 GLU cc_start: 0.7978 (tp30) cc_final: 0.7753 (tp30) REVERT: B 258 TYR cc_start: 0.7428 (t80) cc_final: 0.7143 (t80) REVERT: B 444 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.7690 (m170) REVERT: B 460 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7669 (t80) REVERT: B 628 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7651 (t70) REVERT: B 687 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7661 (tt) REVERT: B 735 ARG cc_start: 0.8593 (ttm170) cc_final: 0.8241 (ttp-170) outliers start: 79 outliers final: 50 residues processed: 186 average time/residue: 0.2239 time to fit residues: 58.2306 Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 107 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.124664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100447 restraints weight = 14137.036| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.62 r_work: 0.2929 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10230 Z= 0.148 Angle : 0.610 12.673 13894 Z= 0.299 Chirality : 0.043 0.178 1594 Planarity : 0.004 0.042 1728 Dihedral : 6.421 85.863 1430 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.63 % Allowed : 32.93 % Favored : 61.44 % 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: -2.37 (0.23), residues: 1260 helix: -1.11 (0.21), residues: 598 sheet: -2.49 (0.54), residues: 80 loop : -1.84 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 125 HIS 0.004 0.001 HIS A 444 PHE 0.011 0.001 PHE A 607 TYR 0.011 0.001 TYR A 766 ARG 0.002 0.000 ARG A 704 Details of bonding type rmsd hydrogen bonds : bond 0.03766 ( 307) hydrogen bonds : angle 4.35291 ( 888) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.36006 ( 4) covalent geometry : bond 0.00361 (10228) covalent geometry : angle 0.61045 (13890) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 1.077 Fit side-chains REVERT: A 168 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 272 ARG cc_start: 0.6456 (OUTLIER) cc_final: 0.5202 (tpp-160) REVERT: A 563 ASP cc_start: 0.7939 (t0) cc_final: 0.7629 (t0) REVERT: A 687 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7597 (tt) REVERT: A 709 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8217 (tt) REVERT: B 119 LEU cc_start: 0.8743 (tp) cc_final: 0.8337 (tt) REVERT: B 168 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8321 (mt) REVERT: B 172 GLU cc_start: 0.7979 (tp30) cc_final: 0.7739 (tp30) REVERT: B 444 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7746 (m170) REVERT: B 460 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7699 (t80) REVERT: B 628 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7685 (t70) REVERT: B 687 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7499 (tt) REVERT: B 735 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8282 (ttp-170) outliers start: 61 outliers final: 47 residues processed: 178 average time/residue: 0.2308 time to fit residues: 57.5560 Evaluate side-chains 173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 118 optimal weight: 0.0980 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102100 restraints weight = 13947.956| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.61 r_work: 0.2943 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10230 Z= 0.121 Angle : 0.592 12.435 13894 Z= 0.290 Chirality : 0.043 0.285 1594 Planarity : 0.004 0.041 1728 Dihedral : 6.095 82.609 1430 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 5.54 % Allowed : 33.58 % Favored : 60.89 % 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: -2.24 (0.23), residues: 1260 helix: -0.96 (0.22), residues: 604 sheet: -2.47 (0.55), residues: 80 loop : -1.83 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 125 HIS 0.003 0.001 HIS A 444 PHE 0.010 0.001 PHE A 607 TYR 0.010 0.001 TYR B 766 ARG 0.001 0.000 ARG A 704 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 307) hydrogen bonds : angle 4.15374 ( 888) SS BOND : bond 0.00070 ( 2) SS BOND : angle 0.30404 ( 4) covalent geometry : bond 0.00290 (10228) covalent geometry : angle 0.59194 (13890) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 125 time to evaluate : 1.045 Fit side-chains REVERT: A 168 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8248 (mt) REVERT: A 272 ARG cc_start: 0.6379 (OUTLIER) cc_final: 0.5177 (tpp-160) REVERT: A 563 ASP cc_start: 0.7949 (t0) cc_final: 0.7657 (t0) REVERT: A 687 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 709 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8193 (tt) REVERT: B 168 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 172 GLU cc_start: 0.7930 (tp30) cc_final: 0.7715 (tp30) REVERT: B 258 TYR cc_start: 0.7124 (t80) cc_final: 0.6259 (m-80) REVERT: B 460 TYR cc_start: 0.8333 (OUTLIER) cc_final: 0.7719 (t80) REVERT: B 628 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7779 (t70) REVERT: B 687 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7510 (tt) REVERT: B 735 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8258 (ttp-170) outliers start: 60 outliers final: 47 residues processed: 175 average time/residue: 0.2231 time to fit residues: 54.6300 Evaluate side-chains 174 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 1.9990 chunk 117 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 38 optimal weight: 0.0170 chunk 125 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.128593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.104606 restraints weight = 13878.796| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.56 r_work: 0.3005 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10230 Z= 0.111 Angle : 0.577 11.898 13894 Z= 0.281 Chirality : 0.041 0.165 1594 Planarity : 0.004 0.039 1728 Dihedral : 5.891 82.425 1430 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 5.44 % Allowed : 34.04 % Favored : 60.52 % 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: -2.11 (0.23), residues: 1260 helix: -0.81 (0.22), residues: 604 sheet: -2.47 (0.55), residues: 80 loop : -1.82 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 125 HIS 0.002 0.001 HIS B 257 PHE 0.010 0.001 PHE A 607 TYR 0.010 0.001 TYR A 766 ARG 0.001 0.000 ARG A 704 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 307) hydrogen bonds : angle 4.09033 ( 888) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.28228 ( 4) covalent geometry : bond 0.00267 (10228) covalent geometry : angle 0.57666 (13890) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 1.074 Fit side-chains REVERT: A 168 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8150 (mt) REVERT: A 272 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5153 (tpp-160) REVERT: A 563 ASP cc_start: 0.7961 (t0) cc_final: 0.7713 (t0) REVERT: A 687 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 709 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8228 (tt) REVERT: B 168 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 258 TYR cc_start: 0.7064 (t80) cc_final: 0.6322 (m-80) REVERT: B 460 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.7647 (t80) REVERT: B 628 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7780 (t70) REVERT: B 687 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7574 (tt) REVERT: B 735 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8277 (ttp-170) outliers start: 59 outliers final: 49 residues processed: 177 average time/residue: 0.2173 time to fit residues: 54.3347 Evaluate side-chains 179 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 541 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 787 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0370 chunk 75 optimal weight: 0.2980 chunk 73 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.1658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.108016 restraints weight = 13792.643| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.53 r_work: 0.3074 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10230 Z= 0.090 Angle : 0.559 12.187 13894 Z= 0.271 Chirality : 0.041 0.165 1594 Planarity : 0.004 0.037 1728 Dihedral : 5.520 77.437 1430 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 4.06 % Allowed : 35.70 % Favored : 60.24 % 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: -1.86 (0.24), residues: 1260 helix: -0.60 (0.22), residues: 598 sheet: -2.36 (0.57), residues: 80 loop : -1.69 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 125 HIS 0.003 0.000 HIS B 283 PHE 0.007 0.001 PHE A 607 TYR 0.020 0.001 TYR A 736 ARG 0.001 0.000 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.02646 ( 307) hydrogen bonds : angle 3.83599 ( 888) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.25694 ( 4) covalent geometry : bond 0.00202 (10228) covalent geometry : angle 0.55931 (13890) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.157 Fit side-chains REVERT: A 73 TYR cc_start: 0.7648 (m-80) cc_final: 0.6952 (m-80) REVERT: A 563 ASP cc_start: 0.7903 (t0) cc_final: 0.7703 (t0) REVERT: A 687 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7671 (tt) REVERT: A 709 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8211 (tt) REVERT: B 168 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 258 TYR cc_start: 0.6940 (t80) cc_final: 0.6331 (m-80) REVERT: B 460 TYR cc_start: 0.8279 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 628 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7839 (t70) REVERT: B 735 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8246 (ttp-170) outliers start: 44 outliers final: 31 residues processed: 169 average time/residue: 0.2211 time to fit residues: 52.3037 Evaluate side-chains 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 460 TYR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 628 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 695 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 120 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.0670 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.103697 restraints weight = 13871.087| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.56 r_work: 0.3021 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10230 Z= 0.124 Angle : 0.588 11.946 13894 Z= 0.285 Chirality : 0.042 0.180 1594 Planarity : 0.004 0.039 1728 Dihedral : 5.634 83.091 1428 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.69 % Allowed : 35.70 % Favored : 60.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.92 (0.23), residues: 1260 helix: -0.57 (0.22), residues: 602 sheet: -2.41 (0.56), residues: 80 loop : -1.81 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 125 HIS 0.003 0.001 HIS B 257 PHE 0.012 0.001 PHE A 607 TYR 0.010 0.001 TYR A 766 ARG 0.002 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 307) hydrogen bonds : angle 3.93926 ( 888) SS BOND : bond 0.00065 ( 2) SS BOND : angle 0.27416 ( 4) covalent geometry : bond 0.00303 (10228) covalent geometry : angle 0.58793 (13890) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4606.30 seconds wall clock time: 80 minutes 53.16 seconds (4853.16 seconds total)