Starting phenix.real_space_refine on Wed Sep 17 17:29:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0i_39704/09_2025/8z0i_39704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0i_39704/09_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_39704/09_2025/8z0i_39704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0i_39704/09_2025/8z0i_39704.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0i_39704/09_2025/8z0i_39704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0i_39704/09_2025/8z0i_39704.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.22, per 1000 atoms: 0.22 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: 0.76 Conformation dependent library (CDL) restraints added in 400.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.26 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: 1.20 Time building geometry restraints manager: 1.03 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: 0.02 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: 4.780 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.560 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG B 116 TYR 0.013 0.001 TYR A 766 PHE 0.008 0.001 PHE A 607 TRP 0.024 0.001 TRP B 125 HIS 0.003 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00375 (10228) covalent geometry : angle 0.61223 (13890) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.34868 ( 4) hydrogen bonds : bond 0.28204 ( 307) hydrogen bonds : angle 8.43280 ( 888) *********************** 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 : 0.313 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: 0.1084 time to fit residues: 21.9222 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 : 0.408 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 123 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 542 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103574 restraints weight = 13826.977| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.50 r_work: 0.3033 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1094 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= 0.112 Angle : 0.555 9.704 13894 Z= 0.281 Chirality : 0.041 0.192 1594 Planarity : 0.004 0.039 1728 Dihedral : 7.827 78.114 1435 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.43 % Allowed : 32.75 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.23), residues: 1260 helix: -1.52 (0.21), residues: 596 sheet: -1.94 (0.51), residues: 104 loop : -1.71 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 470 TYR 0.017 0.001 TYR A 736 PHE 0.008 0.001 PHE A 607 TRP 0.018 0.001 TRP B 125 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00261 (10228) covalent geometry : angle 0.55539 (13890) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.30869 ( 4) hydrogen bonds : bond 0.04499 ( 307) hydrogen bonds : angle 4.98080 ( 888) *********************** 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 193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.386 Fit side-chains REVERT: A 398 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 709 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 735 ARG cc_start: 0.8427 (ttp-170) cc_final: 0.8124 (ttm170) REVERT: B 168 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.7967 (mt) outliers start: 48 outliers final: 22 residues processed: 183 average time/residue: 0.1044 time to fit residues: 27.0660 Evaluate side-chains 153 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 242 VAL 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 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 690 MET Chi-restraints excluded: chain A residue 709 LEU 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 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 473 ASN Chi-restraints excluded: chain B residue 515 VAL 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 682 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 B 499 HIS B 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099862 restraints weight = 14109.650| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.55 r_work: 0.2961 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10230 Z= 0.208 Angle : 0.649 15.355 13894 Z= 0.321 Chirality : 0.044 0.239 1594 Planarity : 0.004 0.041 1728 Dihedral : 7.322 81.003 1430 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.90 % Allowed : 32.29 % Favored : 61.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.23), residues: 1260 helix: -1.40 (0.21), residues: 596 sheet: -2.08 (0.60), residues: 74 loop : -1.85 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 535 TYR 0.013 0.001 TYR A 736 PHE 0.015 0.001 PHE A 607 TRP 0.014 0.001 TRP B 125 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00516 (10228) covalent geometry : angle 0.64940 (13890) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.36630 ( 4) hydrogen bonds : bond 0.04839 ( 307) hydrogen bonds : angle 4.74052 ( 888) *********************** 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 192 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 128 time to evaluate : 0.331 Fit side-chains REVERT: A 398 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8283 (tt) REVERT: A 474 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8246 (t0) REVERT: A 563 ASP cc_start: 0.7785 (t0) cc_final: 0.7436 (t0) REVERT: A 704 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7321 (mtp-110) REVERT: A 709 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8269 (tt) REVERT: B 168 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8480 (mt) REVERT: B 258 TYR cc_start: 0.7276 (t80) cc_final: 0.6936 (t80) outliers start: 64 outliers final: 40 residues processed: 181 average time/residue: 0.0967 time to fit residues: 24.7835 Evaluate side-chains 170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 213 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 409 VAL Chi-restraints excluded: chain A residue 421 MET 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 690 MET 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 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 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 542 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 699 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 42 optimal weight: 0.0980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102448 restraints weight = 14045.868| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.56 r_work: 0.3013 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1342 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 : 0.593 13.958 13894 Z= 0.290 Chirality : 0.042 0.245 1594 Planarity : 0.004 0.040 1728 Dihedral : 6.802 77.359 1430 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.00 % Allowed : 32.01 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.23), residues: 1260 helix: -1.20 (0.21), residues: 598 sheet: -2.33 (0.57), residues: 80 loop : -1.79 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 535 TYR 0.011 0.001 TYR A 736 PHE 0.011 0.001 PHE A 607 TRP 0.013 0.001 TRP A 125 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00314 (10228) covalent geometry : angle 0.59259 (13890) SS BOND : bond 0.00098 ( 2) SS BOND : angle 0.32824 ( 4) hydrogen bonds : bond 0.03808 ( 307) hydrogen bonds : angle 4.39135 ( 888) *********************** 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 201 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.433 Fit side-chains REVERT: A 398 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8142 (tt) REVERT: A 563 ASP cc_start: 0.7784 (t0) cc_final: 0.7437 (t0) REVERT: A 687 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 709 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8185 (tt) REVERT: B 168 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8233 (mt) REVERT: B 444 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7621 (m170) REVERT: B 460 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 65 outliers final: 35 residues processed: 190 average time/residue: 0.1036 time to fit residues: 27.6246 Evaluate side-chains 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL 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 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 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 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 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 138 VAL 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 548 ILE Chi-restraints excluded: chain B residue 602 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 35 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.098222 restraints weight = 14132.250| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.60 r_work: 0.2948 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10230 Z= 0.203 Angle : 0.649 13.950 13894 Z= 0.320 Chirality : 0.045 0.262 1594 Planarity : 0.004 0.042 1728 Dihedral : 6.748 87.602 1430 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 6.27 % Allowed : 32.38 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.23), residues: 1260 helix: -1.28 (0.21), residues: 598 sheet: -2.15 (0.59), residues: 74 loop : -1.91 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 704 TYR 0.018 0.001 TYR B 258 PHE 0.014 0.001 PHE A 607 TRP 0.012 0.001 TRP A 125 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00503 (10228) covalent geometry : angle 0.64897 (13890) SS BOND : bond 0.00143 ( 2) SS BOND : angle 0.39859 ( 4) hydrogen bonds : bond 0.04386 ( 307) hydrogen bonds : angle 4.49997 ( 888) *********************** 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 194 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 126 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 272 ARG cc_start: 0.6727 (OUTLIER) cc_final: 0.5915 (tpp-160) REVERT: A 398 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8205 (tt) REVERT: A 444 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.7578 (m-70) REVERT: A 474 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8335 (t0) REVERT: A 530 ASP cc_start: 0.8058 (t70) cc_final: 0.7851 (t70) REVERT: A 563 ASP cc_start: 0.7892 (t0) cc_final: 0.7567 (t0) REVERT: A 687 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7700 (tt) REVERT: A 704 ARG cc_start: 0.7441 (mtp85) cc_final: 0.6945 (mtm110) REVERT: A 709 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8236 (tt) REVERT: B 168 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8457 (mt) REVERT: B 172 GLU cc_start: 0.7954 (tp30) cc_final: 0.7735 (tp30) REVERT: B 444 HIS cc_start: 0.8479 (OUTLIER) cc_final: 0.7815 (m170) REVERT: B 460 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.7693 (t80) REVERT: B 542 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8376 (t0) REVERT: B 628 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7645 (t70) REVERT: B 687 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7601 (tt) REVERT: B 735 ARG cc_start: 0.8531 (ttm170) cc_final: 0.8180 (ttp-170) outliers start: 68 outliers final: 49 residues processed: 182 average time/residue: 0.1035 time to fit residues: 26.3131 Evaluate side-chains 183 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 122 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 114 VAL 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 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 415 ILE 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 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 213 LEU 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 495 VAL 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 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 787 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 ASN B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.100606 restraints weight = 14073.538| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.64 r_work: 0.2895 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1447 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= 0.172 Angle : 0.621 13.339 13894 Z= 0.307 Chirality : 0.043 0.204 1594 Planarity : 0.004 0.043 1728 Dihedral : 6.608 89.689 1430 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 7.56 % Allowed : 31.64 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.23), residues: 1260 helix: -1.18 (0.21), residues: 598 sheet: -2.41 (0.56), residues: 80 loop : -1.88 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 535 TYR 0.017 0.001 TYR B 258 PHE 0.013 0.001 PHE A 607 TRP 0.013 0.001 TRP B 125 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00423 (10228) covalent geometry : angle 0.62085 (13890) SS BOND : bond 0.00128 ( 2) SS BOND : angle 0.38262 ( 4) hydrogen bonds : bond 0.04043 ( 307) hydrogen bonds : angle 4.40943 ( 888) *********************** 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 206 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 124 time to evaluate : 0.388 Fit side-chains REVERT: A 168 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8412 (mt) REVERT: A 272 ARG cc_start: 0.6612 (OUTLIER) cc_final: 0.5720 (tpp-160) REVERT: A 398 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8165 (tt) REVERT: A 444 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7460 (m-70) REVERT: A 474 ASN cc_start: 0.8480 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 563 ASP cc_start: 0.7958 (t0) cc_final: 0.7621 (t0) REVERT: A 687 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7606 (tt) REVERT: A 709 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8232 (tt) REVERT: B 168 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8370 (mt) REVERT: B 172 GLU cc_start: 0.7902 (tp30) cc_final: 0.7656 (tp30) REVERT: B 258 TYR cc_start: 0.7492 (t80) cc_final: 0.7220 (t80) REVERT: B 444 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7776 (m170) REVERT: B 460 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7671 (t80) REVERT: B 542 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8462 (t0) REVERT: B 628 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7725 (t70) REVERT: B 687 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7496 (tt) REVERT: B 735 ARG cc_start: 0.8531 (ttm170) cc_final: 0.8158 (ttp-170) outliers start: 82 outliers final: 57 residues processed: 193 average time/residue: 0.0999 time to fit residues: 27.3158 Evaluate side-chains 190 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 120 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 138 VAL 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 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 415 ILE 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 473 ASN Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 495 VAL 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 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 737 VAL 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 177 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 213 LEU 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 495 VAL 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 542 ASN 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 787 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 52 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.124992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.100831 restraints weight = 13918.606| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.61 r_work: 0.2924 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10230 Z= 0.140 Angle : 0.601 12.885 13894 Z= 0.296 Chirality : 0.043 0.255 1594 Planarity : 0.004 0.041 1728 Dihedral : 6.407 87.097 1430 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 6.83 % Allowed : 32.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.23), residues: 1260 helix: -1.07 (0.22), residues: 598 sheet: -2.40 (0.56), residues: 80 loop : -1.85 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 704 TYR 0.015 0.001 TYR B 258 PHE 0.011 0.001 PHE A 607 TRP 0.015 0.001 TRP B 125 HIS 0.003 0.001 HIS A 444 Details of bonding type rmsd covalent geometry : bond 0.00342 (10228) covalent geometry : angle 0.60126 (13890) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.33648 ( 4) hydrogen bonds : bond 0.03720 ( 307) hydrogen bonds : angle 4.28524 ( 888) *********************** 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 199 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.398 Fit side-chains REVERT: A 168 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8303 (mt) REVERT: A 272 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5644 (tpp-160) REVERT: A 398 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 474 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8200 (t0) REVERT: A 563 ASP cc_start: 0.7922 (t0) cc_final: 0.7605 (t0) REVERT: A 687 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7598 (tt) REVERT: A 704 ARG cc_start: 0.7515 (mtp85) cc_final: 0.7012 (mtm110) REVERT: A 709 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8194 (tt) REVERT: B 168 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (mt) REVERT: B 172 GLU cc_start: 0.7987 (tp30) cc_final: 0.7738 (tp30) REVERT: B 258 TYR cc_start: 0.7491 (t80) cc_final: 0.7219 (t80) REVERT: B 444 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7753 (m170) REVERT: B 460 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 542 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8266 (t0) REVERT: B 628 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7762 (t70) REVERT: B 687 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7508 (tt) REVERT: B 735 ARG cc_start: 0.8534 (ttm170) cc_final: 0.8287 (ttp-170) outliers start: 74 outliers final: 56 residues processed: 184 average time/residue: 0.1049 time to fit residues: 27.0965 Evaluate side-chains 191 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 123 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 138 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 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 415 ILE Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 473 ASN 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 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 737 VAL 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 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 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 542 ASN 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 787 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.126019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101935 restraints weight = 13890.605| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.60 r_work: 0.2940 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1555 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= 0.122 Angle : 0.593 12.672 13894 Z= 0.289 Chirality : 0.042 0.277 1594 Planarity : 0.004 0.041 1728 Dihedral : 6.238 85.096 1430 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 6.27 % Allowed : 32.93 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.23), residues: 1260 helix: -0.98 (0.22), residues: 602 sheet: -2.40 (0.56), residues: 80 loop : -1.85 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.013 0.001 TYR B 258 PHE 0.010 0.001 PHE A 607 TRP 0.022 0.001 TRP B 125 HIS 0.002 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00294 (10228) covalent geometry : angle 0.59294 (13890) SS BOND : bond 0.00090 ( 2) SS BOND : angle 0.32296 ( 4) hydrogen bonds : bond 0.03477 ( 307) hydrogen bonds : angle 4.18143 ( 888) *********************** 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 193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 125 time to evaluate : 0.393 Fit side-chains REVERT: A 168 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 272 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5641 (tpp-160) REVERT: A 398 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8127 (tt) REVERT: A 563 ASP cc_start: 0.7926 (t0) cc_final: 0.7623 (t0) REVERT: A 687 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7553 (tt) REVERT: A 709 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8178 (tt) REVERT: B 168 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8176 (mt) REVERT: B 172 GLU cc_start: 0.7958 (tp30) cc_final: 0.7710 (tp30) REVERT: B 258 TYR cc_start: 0.7404 (t80) cc_final: 0.7112 (t80) REVERT: B 460 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7694 (t80) REVERT: B 628 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7753 (t70) REVERT: B 687 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7511 (tt) REVERT: B 735 ARG cc_start: 0.8496 (ttm170) cc_final: 0.8250 (ttp-170) outliers start: 68 outliers final: 50 residues processed: 181 average time/residue: 0.1056 time to fit residues: 26.9522 Evaluate side-chains 179 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 120 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 138 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 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 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 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 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 405 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.3980 chunk 118 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 473 ASN A 474 ASN B 542 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.127359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103299 restraints weight = 13813.693| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.59 r_work: 0.2971 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1618 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= 0.126 Angle : 0.595 13.795 13894 Z= 0.289 Chirality : 0.042 0.179 1594 Planarity : 0.004 0.040 1728 Dihedral : 6.076 84.717 1430 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 6.09 % Allowed : 33.12 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.23), residues: 1260 helix: -0.88 (0.22), residues: 600 sheet: -2.43 (0.55), residues: 80 loop : -1.85 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 704 TYR 0.010 0.001 TYR A 766 PHE 0.011 0.001 PHE A 607 TRP 0.024 0.001 TRP B 125 HIS 0.003 0.001 HIS B 444 Details of bonding type rmsd covalent geometry : bond 0.00306 (10228) covalent geometry : angle 0.59512 (13890) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.35520 ( 4) hydrogen bonds : bond 0.03411 ( 307) hydrogen bonds : angle 4.15314 ( 888) *********************** 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 191 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 125 time to evaluate : 0.322 Fit side-chains REVERT: A 168 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 272 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.5576 (tpp-160) REVERT: A 398 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8168 (tt) REVERT: A 474 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8118 (t0) REVERT: A 563 ASP cc_start: 0.7889 (t0) cc_final: 0.7641 (t0) REVERT: A 687 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7584 (tt) REVERT: A 709 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8187 (tt) REVERT: B 168 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8211 (mt) REVERT: B 172 GLU cc_start: 0.7983 (tp30) cc_final: 0.7731 (tp30) REVERT: B 460 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7667 (t80) REVERT: B 542 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8267 (t0) REVERT: B 628 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7764 (t70) REVERT: B 687 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7547 (tt) REVERT: B 735 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8259 (ttp-170) outliers start: 66 outliers final: 53 residues processed: 182 average time/residue: 0.0977 time to fit residues: 25.0988 Evaluate side-chains 184 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 120 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 138 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 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 415 ILE 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 474 ASN 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 157 SER 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 541 SER Chi-restraints excluded: chain B residue 542 ASN 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 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 96 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 105 optimal weight: 0.0470 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 474 ASN B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102914 restraints weight = 13664.083| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.56 r_work: 0.2971 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1647 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= 0.123 Angle : 0.599 13.770 13894 Z= 0.290 Chirality : 0.042 0.175 1594 Planarity : 0.004 0.039 1728 Dihedral : 6.014 84.001 1430 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 6.46 % Allowed : 32.75 % Favored : 60.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.23), residues: 1260 helix: -0.79 (0.22), residues: 600 sheet: -2.42 (0.56), residues: 80 loop : -1.85 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 206 TYR 0.010 0.001 TYR B 766 PHE 0.010 0.001 PHE A 607 TRP 0.023 0.001 TRP B 125 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00299 (10228) covalent geometry : angle 0.59878 (13890) SS BOND : bond 0.00078 ( 2) SS BOND : angle 0.30074 ( 4) hydrogen bonds : bond 0.03356 ( 307) hydrogen bonds : angle 4.11066 ( 888) ********************** 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 192 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 122 time to evaluate : 0.308 Fit side-chains REVERT: A 168 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8174 (mt) REVERT: A 272 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.5578 (tpp-160) REVERT: A 398 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8167 (tt) REVERT: A 563 ASP cc_start: 0.7887 (t0) cc_final: 0.7638 (t0) REVERT: A 687 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 709 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 168 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8162 (mt) REVERT: B 172 GLU cc_start: 0.7976 (tp30) cc_final: 0.7725 (tp30) REVERT: B 258 TYR cc_start: 0.6876 (t80) cc_final: 0.6518 (m-80) REVERT: B 460 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7664 (t80) REVERT: B 628 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7757 (t70) REVERT: B 687 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7536 (tt) REVERT: B 735 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8257 (ttp-170) outliers start: 70 outliers final: 54 residues processed: 184 average time/residue: 0.0986 time to fit residues: 25.6983 Evaluate side-chains 182 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 119 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain A residue 138 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 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 415 ILE 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 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 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 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 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 542 ASN 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 45 optimal weight: 0.0570 chunk 78 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.4700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 474 ASN B 542 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.127409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103173 restraints weight = 13911.669| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.61 r_work: 0.2973 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1707 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= 0.116 Angle : 0.598 13.388 13894 Z= 0.288 Chirality : 0.043 0.297 1594 Planarity : 0.004 0.039 1728 Dihedral : 5.905 83.018 1430 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.81 % Allowed : 33.21 % Favored : 60.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.23), residues: 1260 helix: -0.71 (0.22), residues: 598 sheet: -2.41 (0.56), residues: 80 loop : -1.84 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 704 TYR 0.010 0.001 TYR A 766 PHE 0.010 0.001 PHE A 607 TRP 0.024 0.001 TRP B 125 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00278 (10228) covalent geometry : angle 0.59803 (13890) SS BOND : bond 0.00066 ( 2) SS BOND : angle 0.30815 ( 4) hydrogen bonds : bond 0.03251 ( 307) hydrogen bonds : angle 4.05942 ( 888) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2064.30 seconds wall clock time: 36 minutes 11.85 seconds (2171.85 seconds total)