Starting phenix.real_space_refine on Thu May 1 01:17:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.map" model { file = "/net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z0j_39705/05_2025/8z0j_39705.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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 6476 2.51 5 N 1666 2.21 5 O 1798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4976 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 25, 'TRANS': 609} Chain breaks: 1 Chain: "B" Number of atoms: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 4976 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 25, 'TRANS': 609} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.53, per 1000 atoms: 0.65 Number of scatterers: 10016 At special positions: 0 Unit cell: (86.994, 78.402, 151.434, 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 1798 8.00 N 1666 7.00 C 6476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 462 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 462 " - pdb=" SG CYS B 568 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 51.4% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.919A pdb=" N PHE A 165 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.183A pdb=" N ASN A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.684A pdb=" N ARG A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 239 removed outlier: 3.621A pdb=" N SER A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.870A pdb=" N GLN A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 265 removed outlier: 4.143A pdb=" N ARG A 263 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN A 264 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.616A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.667A pdb=" N PHE A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 416 " --> pdb=" O MET A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 removed outlier: 3.660A pdb=" N ILE A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.676A 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 497 removed outlier: 4.036A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 521 removed outlier: 3.576A pdb=" N ALA A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) 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 566 removed outlier: 3.655A pdb=" N ILE A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 555 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 558 " --> pdb=" O GLN A 554 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 614 Proline residue: A 599 - end of helix removed outlier: 6.592A pdb=" N LEU A 603 " --> pdb=" O PRO A 599 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 633 removed outlier: 4.020A pdb=" N VAL A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 633 " --> pdb=" O ARG A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 665 removed outlier: 3.775A pdb=" N ILE A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 641 " --> pdb=" O PRO A 637 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 648 " --> pdb=" O HIS A 644 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 651 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 654 " --> pdb=" O VAL A 650 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A 655 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 700 removed outlier: 3.670A pdb=" N VAL A 678 " --> pdb=" O ASP A 674 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 679 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 686 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 694 " --> pdb=" O MET A 690 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 695 " --> pdb=" O CYS A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 712 removed outlier: 3.985A pdb=" N ILE A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.994A pdb=" N THR A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 749 " --> pdb=" O LEU A 745 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 755 " --> pdb=" O ARG A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 765 through 789 removed outlier: 4.027A pdb=" N PHE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N TRP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER A 783 " --> pdb=" O PHE A 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.876A pdb=" N MET B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 165 " --> pdb=" O THR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.970A pdb=" N ASN B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.589A pdb=" N ARG B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B 207 " --> pdb=" O GLN B 203 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 208 " --> pdb=" O GLN B 204 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 removed outlier: 3.639A pdb=" N LEU B 241 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL B 242 " --> pdb=" O TRP B 238 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 243 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 removed outlier: 4.382A pdb=" N GLN B 264 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 265 " --> pdb=" O ALA B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.547A pdb=" N LEU B 286 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.599A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.798A 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 497 removed outlier: 3.993A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 496 " --> pdb=" O VAL B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 519 removed outlier: 3.501A pdb=" N ARG B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.588A pdb=" N GLN B 531 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 569 removed outlier: 3.962A pdb=" N ILE B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 555 " --> pdb=" O ARG B 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 558 " --> pdb=" O GLN B 554 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 567 " --> pdb=" O ASP B 563 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS B 568 " --> pdb=" O LEU B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 597 removed outlier: 3.738A pdb=" N PHE B 596 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 597 " --> pdb=" O PHE B 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 592 through 597' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.850A pdb=" N LEU B 603 " --> pdb=" O PRO B 599 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 633 removed outlier: 4.056A pdb=" N VAL B 632 " --> pdb=" O ASP B 628 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 665 removed outlier: 3.804A pdb=" N ILE B 640 " --> pdb=" O THR B 636 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 641 " --> pdb=" O PRO B 637 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 642 " --> pdb=" O GLY B 638 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY B 654 " --> pdb=" O VAL B 650 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 700 removed outlier: 3.746A pdb=" N VAL B 678 " --> pdb=" O ASP B 674 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 679 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 694 " --> pdb=" O MET B 690 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 695 " --> pdb=" O CYS B 691 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 696 " --> pdb=" O PHE B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.668A pdb=" N ALA B 706 " --> pdb=" O LEU B 702 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 707 " --> pdb=" O GLU B 703 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU B 709 " --> pdb=" O ASN B 705 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA B 710 " --> pdb=" O ALA B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 721 removed outlier: 3.884A pdb=" N THR B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 721 " --> pdb=" O THR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 730 removed outlier: 3.875A pdb=" N MET B 730 " --> pdb=" O ILE B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 743 through 755 removed outlier: 3.771A pdb=" N THR B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B 755 " --> pdb=" O ARG B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 790 removed outlier: 3.501A pdb=" N TYR B 766 " --> pdb=" O GLU B 762 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 767 " --> pdb=" O PRO B 763 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TRP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 776 " --> pdb=" O THR B 772 " (cutoff:3.500A) removed outlier: 3.798A 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: 3.631A pdb=" N MET A 88 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 66 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 64 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 97 removed outlier: 3.902A pdb=" N ASP A 223 " --> pdb=" O MET A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 271 removed outlier: 6.488A pdb=" N LEU A 270 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441 Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 535 removed outlier: 5.680A pdb=" N VAL A 534 " --> pdb=" O SER B 580 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.496A pdb=" N SER A 580 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU B 538 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 90 removed outlier: 3.583A pdb=" N MET B 88 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 66 " --> pdb=" O MET B 88 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 64 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 99 removed outlier: 5.862A pdb=" N GLY B 269 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 270 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 437 through 441 345 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3158 1.34 - 1.46: 2357 1.46 - 1.58: 4606 1.58 - 1.70: 11 1.70 - 1.81: 108 Bond restraints: 10240 Sorted by residual: bond pdb=" CB PRO A 763 " pdb=" CG PRO A 763 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.38e+00 bond pdb=" CA SER A 390 " pdb=" CB SER A 390 " ideal model delta sigma weight residual 1.530 1.493 0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" CG PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 1.503 1.563 -0.060 3.40e-02 8.65e+02 3.10e+00 bond pdb=" CB PRO B 599 " pdb=" CG PRO B 599 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.91e+00 bond pdb=" C GLN B 224 " pdb=" N PRO B 225 " ideal model delta sigma weight residual 1.333 1.345 -0.012 7.80e-03 1.64e+04 2.50e+00 ... (remaining 10235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.07: 13833 3.07 - 6.14: 59 6.14 - 9.22: 13 9.22 - 12.29: 0 12.29 - 15.36: 1 Bond angle restraints: 13906 Sorted by residual: angle pdb=" CA PRO A 763 " pdb=" N PRO A 763 " pdb=" CD PRO A 763 " ideal model delta sigma weight residual 112.00 103.47 8.53 1.40e+00 5.10e-01 3.71e+01 angle pdb=" CA ARG A 272 " pdb=" C ARG A 272 " pdb=" N SER A 273 " ideal model delta sigma weight residual 119.46 116.17 3.29 6.10e-01 2.69e+00 2.90e+01 angle pdb=" N ARG A 272 " pdb=" CA ARG A 272 " pdb=" C ARG A 272 " ideal model delta sigma weight residual 108.48 101.03 7.45 1.65e+00 3.67e-01 2.04e+01 angle pdb=" CA LEU B 529 " pdb=" CB LEU B 529 " pdb=" CG LEU B 529 " ideal model delta sigma weight residual 116.30 131.66 -15.36 3.50e+00 8.16e-02 1.93e+01 angle pdb=" CA PRO B 599 " pdb=" N PRO B 599 " pdb=" CD PRO B 599 " ideal model delta sigma weight residual 112.00 106.01 5.99 1.40e+00 5.10e-01 1.83e+01 ... (remaining 13901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5000 17.59 - 35.18: 785 35.18 - 52.78: 248 52.78 - 70.37: 45 70.37 - 87.96: 10 Dihedral angle restraints: 6088 sinusoidal: 2448 harmonic: 3640 Sorted by residual: 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 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TRP B 167 " pdb=" C TRP B 167 " pdb=" N ILE B 168 " pdb=" CA ILE B 168 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+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 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 6085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1339 0.053 - 0.106: 237 0.106 - 0.159: 17 0.159 - 0.212: 2 0.212 - 0.265: 1 Chirality restraints: 1596 Sorted by residual: chirality pdb=" CA ARG A 272 " pdb=" N ARG A 272 " pdb=" C ARG A 272 " pdb=" CB ARG A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA PRO A 763 " pdb=" N PRO A 763 " pdb=" C PRO A 763 " pdb=" CB PRO A 763 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CB ILE B 253 " pdb=" CA ILE B 253 " pdb=" CG1 ILE B 253 " pdb=" CG2 ILE B 253 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1593 not shown) Planarity restraints: 1730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 598 " 0.074 5.00e-02 4.00e+02 1.09e-01 1.92e+01 pdb=" N PRO B 599 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 762 " -0.064 5.00e-02 4.00e+02 9.20e-02 1.35e+01 pdb=" N PRO A 763 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 763 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 763 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 525 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO B 526 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 526 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 526 " -0.036 5.00e-02 4.00e+02 ... (remaining 1727 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1959 2.77 - 3.31: 9175 3.31 - 3.84: 15171 3.84 - 4.37: 17986 4.37 - 4.90: 31857 Nonbonded interactions: 76148 Sorted by model distance: nonbonded pdb=" OG SER B 592 " pdb=" OD2 ASP B 595 " model vdw 2.242 3.040 nonbonded pdb=" O LEU A 472 " pdb=" ND2 ASN A 473 " model vdw 2.272 3.120 nonbonded pdb=" OG SER A 200 " pdb=" OE1 GLN A 203 " model vdw 2.274 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP A 595 " model vdw 2.276 3.040 nonbonded pdb=" OG SER B 200 " pdb=" OE1 GLN B 203 " model vdw 2.277 3.040 ... (remaining 76143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.460 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 10242 Z= 0.114 Angle : 0.585 15.360 13910 Z= 0.304 Chirality : 0.040 0.265 1596 Planarity : 0.005 0.109 1730 Dihedral : 18.689 87.960 3750 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.55 % Allowed : 34.07 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.23), residues: 1262 helix: -1.42 (0.20), residues: 626 sheet: -1.32 (0.61), residues: 96 loop : -2.09 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.003 0.000 HIS B 444 PHE 0.013 0.001 PHE B 714 TYR 0.011 0.001 TYR A 766 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.26944 ( 345) hydrogen bonds : angle 8.34743 ( 999) SS BOND : bond 0.00050 ( 2) SS BOND : angle 0.52032 ( 4) covalent geometry : bond 0.00263 (10240) covalent geometry : angle 0.58512 (13906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.009 Fit side-chains REVERT: A 224 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 552 ASP cc_start: 0.7741 (t0) cc_final: 0.7179 (t0) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.2224 time to fit residues: 46.6846 Evaluate side-chains 135 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain B residue 224 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.0170 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 422 GLN A 444 HIS A 474 ASN A 509 ASN A 531 GLN B 542 ASN B 655 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118016 restraints weight = 13030.427| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.30 r_work: 0.3198 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10242 Z= 0.131 Angle : 0.573 14.224 13910 Z= 0.287 Chirality : 0.042 0.138 1596 Planarity : 0.004 0.072 1730 Dihedral : 8.391 88.699 1441 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.70 % Allowed : 30.48 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.23), residues: 1262 helix: -0.96 (0.21), residues: 622 sheet: -2.08 (0.61), residues: 78 loop : -2.09 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.002 0.001 HIS A 240 PHE 0.013 0.001 PHE A 607 TYR 0.014 0.001 TYR A 766 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.05692 ( 345) hydrogen bonds : angle 5.18306 ( 999) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.19247 ( 4) covalent geometry : bond 0.00300 (10240) covalent geometry : angle 0.57346 (13906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 145 time to evaluate : 1.132 Fit side-chains REVERT: A 474 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 224 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: B 243 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 398 LEU cc_start: 0.8560 (tp) cc_final: 0.8298 (tp) REVERT: B 552 ASP cc_start: 0.8478 (t0) cc_final: 0.8114 (t0) REVERT: B 576 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7405 (mm-30) outliers start: 51 outliers final: 32 residues processed: 183 average time/residue: 0.2050 time to fit residues: 54.2220 Evaluate side-chains 170 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 744 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 A 509 ASN B 542 ASN B 644 HIS B 708 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115968 restraints weight = 13261.893| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.30 r_work: 0.3168 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10242 Z= 0.151 Angle : 0.580 13.123 13910 Z= 0.291 Chirality : 0.042 0.151 1596 Planarity : 0.004 0.058 1730 Dihedral : 7.991 88.388 1436 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 5.99 % Allowed : 29.65 % Favored : 64.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1262 helix: -0.89 (0.21), residues: 624 sheet: -2.06 (0.61), residues: 78 loop : -2.13 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 167 HIS 0.014 0.001 HIS A 444 PHE 0.024 0.001 PHE A 789 TYR 0.014 0.001 TYR A 766 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04902 ( 345) hydrogen bonds : angle 4.83032 ( 999) SS BOND : bond 0.00420 ( 2) SS BOND : angle 0.45623 ( 4) covalent geometry : bond 0.00364 (10240) covalent geometry : angle 0.57996 (13906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 142 time to evaluate : 1.211 Fit side-chains REVERT: A 474 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (t0) REVERT: A 702 LEU cc_start: 0.8292 (mp) cc_final: 0.7935 (mt) REVERT: A 750 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8319 (tt) REVERT: B 224 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8108 (mt0) REVERT: B 243 GLN cc_start: 0.8127 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 552 ASP cc_start: 0.8449 (t0) cc_final: 0.8070 (t0) outliers start: 65 outliers final: 43 residues processed: 191 average time/residue: 0.2032 time to fit residues: 56.2738 Evaluate side-chains 179 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 474 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 665 LEU 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 708 GLN Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 727 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 0.0470 chunk 103 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 257 HIS A 444 HIS A 473 ASN B 542 ASN B 708 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117341 restraints weight = 12943.299| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.27 r_work: 0.3192 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10242 Z= 0.116 Angle : 0.556 12.254 13910 Z= 0.276 Chirality : 0.041 0.160 1596 Planarity : 0.004 0.052 1730 Dihedral : 7.666 87.256 1436 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.89 % Allowed : 30.39 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.23), residues: 1262 helix: -0.75 (0.21), residues: 628 sheet: -2.07 (0.60), residues: 78 loop : -2.13 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.005 0.001 HIS A 444 PHE 0.024 0.001 PHE A 789 TYR 0.012 0.001 TYR B 766 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 345) hydrogen bonds : angle 4.58337 ( 999) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.70183 ( 4) covalent geometry : bond 0.00273 (10240) covalent geometry : angle 0.55644 (13906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 140 time to evaluate : 1.126 Fit side-chains REVERT: A 750 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8289 (tt) REVERT: B 178 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 224 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8159 (mt0) REVERT: B 243 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7754 (tm-30) outliers start: 64 outliers final: 46 residues processed: 188 average time/residue: 0.2088 time to fit residues: 56.4723 Evaluate side-chains 181 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 690 MET Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 224 GLN Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 727 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 0.0070 chunk 112 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 66 optimal weight: 0.0770 chunk 120 optimal weight: 0.8980 chunk 56 optimal weight: 0.0770 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.2714 ------------------------------------------------------------------------------- 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 655 GLN B 542 ASN B 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.119304 restraints weight = 13003.308| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.28 r_work: 0.3215 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10242 Z= 0.099 Angle : 0.554 15.495 13910 Z= 0.272 Chirality : 0.041 0.162 1596 Planarity : 0.004 0.047 1730 Dihedral : 7.235 84.879 1433 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 5.52 % Allowed : 30.76 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.23), residues: 1262 helix: -0.56 (0.22), residues: 630 sheet: -2.09 (0.60), residues: 78 loop : -2.04 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 167 HIS 0.010 0.001 HIS A 444 PHE 0.025 0.001 PHE A 789 TYR 0.010 0.001 TYR B 766 ARG 0.001 0.000 ARG A 622 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 345) hydrogen bonds : angle 4.34913 ( 999) SS BOND : bond 0.00030 ( 2) SS BOND : angle 0.66512 ( 4) covalent geometry : bond 0.00222 (10240) covalent geometry : angle 0.55363 (13906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.063 Fit side-chains REVERT: A 487 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: A 750 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8248 (tt) REVERT: B 178 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8463 (tm-30) REVERT: B 243 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 60 outliers final: 41 residues processed: 185 average time/residue: 0.2074 time to fit residues: 55.0378 Evaluate side-chains 175 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 132 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 GLN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 750 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 0.0970 chunk 92 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 78 optimal weight: 0.0170 chunk 113 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 542 ASN B 708 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.140099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116104 restraints weight = 13151.792| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.29 r_work: 0.3175 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10242 Z= 0.151 Angle : 0.590 14.995 13910 Z= 0.291 Chirality : 0.043 0.190 1596 Planarity : 0.004 0.046 1730 Dihedral : 6.747 87.164 1430 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.62 % Allowed : 30.66 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 1262 helix: -0.61 (0.21), residues: 630 sheet: -2.11 (0.60), residues: 78 loop : -2.11 (0.24), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.009 0.001 HIS A 444 PHE 0.025 0.001 PHE A 789 TYR 0.015 0.001 TYR B 766 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 345) hydrogen bonds : angle 4.38922 ( 999) SS BOND : bond 0.00047 ( 2) SS BOND : angle 0.66449 ( 4) covalent geometry : bond 0.00368 (10240) covalent geometry : angle 0.59041 (13906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 133 time to evaluate : 1.034 Fit side-chains REVERT: A 750 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8287 (tt) REVERT: B 178 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 243 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 552 ASP cc_start: 0.8467 (t0) cc_final: 0.8187 (t0) outliers start: 61 outliers final: 50 residues processed: 185 average time/residue: 0.2033 time to fit residues: 54.2612 Evaluate side-chains 184 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 727 ILE Chi-restraints excluded: chain B residue 750 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 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 B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117013 restraints weight = 13064.420| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.27 r_work: 0.3185 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10242 Z= 0.125 Angle : 0.578 14.488 13910 Z= 0.284 Chirality : 0.042 0.200 1596 Planarity : 0.004 0.044 1730 Dihedral : 6.645 86.901 1430 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 6.17 % Allowed : 29.74 % Favored : 64.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.23), residues: 1262 helix: -0.53 (0.22), residues: 628 sheet: -2.17 (0.59), residues: 78 loop : -2.14 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.007 0.001 HIS A 444 PHE 0.026 0.001 PHE A 789 TYR 0.013 0.001 TYR B 766 ARG 0.002 0.000 ARG A 116 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 345) hydrogen bonds : angle 4.32787 ( 999) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.66417 ( 4) covalent geometry : bond 0.00301 (10240) covalent geometry : angle 0.57830 (13906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 138 time to evaluate : 1.223 Fit side-chains REVERT: A 552 ASP cc_start: 0.8575 (t0) cc_final: 0.8311 (t0) REVERT: A 750 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8251 (tt) REVERT: B 243 GLN cc_start: 0.8040 (tm-30) cc_final: 0.7749 (tm-30) outliers start: 67 outliers final: 54 residues processed: 191 average time/residue: 0.2222 time to fit residues: 60.4972 Evaluate side-chains 187 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 665 LEU 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 727 ILE Chi-restraints excluded: chain B residue 750 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 43 optimal weight: 0.0470 chunk 67 optimal weight: 0.3980 chunk 13 optimal weight: 0.0020 chunk 89 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.2644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 542 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120994 restraints weight = 12923.126| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.22 r_work: 0.3218 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10242 Z= 0.101 Angle : 0.566 14.029 13910 Z= 0.277 Chirality : 0.041 0.179 1596 Planarity : 0.004 0.042 1730 Dihedral : 6.367 84.395 1430 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.88 % Allowed : 31.58 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.23), residues: 1262 helix: -0.36 (0.22), residues: 628 sheet: -2.21 (0.58), residues: 78 loop : -2.09 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 167 HIS 0.008 0.001 HIS A 444 PHE 0.027 0.001 PHE A 789 TYR 0.011 0.001 TYR B 766 ARG 0.002 0.000 ARG B 179 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 345) hydrogen bonds : angle 4.19315 ( 999) SS BOND : bond 0.00032 ( 2) SS BOND : angle 0.69062 ( 4) covalent geometry : bond 0.00228 (10240) covalent geometry : angle 0.56620 (13906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 1.183 Fit side-chains REVERT: A 552 ASP cc_start: 0.8535 (t0) cc_final: 0.8283 (t0) REVERT: A 750 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8241 (tt) REVERT: B 178 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8223 (tt0) REVERT: B 243 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7776 (tm-30) outliers start: 53 outliers final: 44 residues processed: 187 average time/residue: 0.2221 time to fit residues: 58.9562 Evaluate side-chains 178 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 133 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 GLN Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 715 TYR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 727 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 570 GLN B 235 GLN B 542 ASN B 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115735 restraints weight = 13108.215| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.28 r_work: 0.3164 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10242 Z= 0.165 Angle : 0.616 14.108 13910 Z= 0.303 Chirality : 0.043 0.171 1596 Planarity : 0.004 0.042 1730 Dihedral : 6.431 87.610 1430 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.52 % Allowed : 30.66 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 1262 helix: -0.52 (0.22), residues: 630 sheet: -2.38 (0.62), residues: 66 loop : -2.20 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 167 HIS 0.019 0.001 HIS A 444 PHE 0.026 0.001 PHE A 789 TYR 0.015 0.001 TYR B 766 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 345) hydrogen bonds : angle 4.31995 ( 999) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.59108 ( 4) covalent geometry : bond 0.00409 (10240) covalent geometry : angle 0.61605 (13906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 1.128 Fit side-chains REVERT: A 552 ASP cc_start: 0.8591 (t0) cc_final: 0.8331 (t0) REVERT: A 750 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8282 (tt) outliers start: 60 outliers final: 51 residues processed: 178 average time/residue: 0.2470 time to fit residues: 63.3576 Evaluate side-chains 179 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 708 GLN Chi-restraints excluded: chain B residue 727 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS A 570 GLN B 235 GLN B 542 ASN B 708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.138295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114245 restraints weight = 13227.343| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.30 r_work: 0.3150 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10242 Z= 0.192 Angle : 0.649 14.303 13910 Z= 0.318 Chirality : 0.044 0.172 1596 Planarity : 0.004 0.041 1730 Dihedral : 6.528 89.367 1430 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.62 % Allowed : 30.76 % Favored : 63.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.23), residues: 1262 helix: -0.67 (0.21), residues: 630 sheet: -2.41 (0.61), residues: 66 loop : -2.27 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.009 0.001 HIS A 444 PHE 0.026 0.002 PHE A 789 TYR 0.017 0.002 TYR A 736 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 345) hydrogen bonds : angle 4.43378 ( 999) SS BOND : bond 0.00083 ( 2) SS BOND : angle 0.60947 ( 4) covalent geometry : bond 0.00473 (10240) covalent geometry : angle 0.64949 (13906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2524 Ramachandran restraints generated. 1262 Oldfield, 0 Emsley, 1262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 131 time to evaluate : 1.223 Fit side-chains REVERT: A 552 ASP cc_start: 0.8597 (t0) cc_final: 0.8336 (t0) REVERT: A 750 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 243 GLN cc_start: 0.8058 (tm-30) cc_final: 0.7737 (tt0) REVERT: B 542 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.7894 (t0) REVERT: B 543 GLN cc_start: 0.7765 (mp10) cc_final: 0.6997 (mp10) REVERT: B 784 MET cc_start: 0.8413 (mmm) cc_final: 0.8119 (mmm) outliers start: 61 outliers final: 54 residues processed: 181 average time/residue: 0.2269 time to fit residues: 59.4182 Evaluate side-chains 188 residues out of total 1086 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 148 GLN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 404 ARG Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 511 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 623 MET Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 684 LEU Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 462 CYS Chi-restraints excluded: chain B residue 473 ASN Chi-restraints excluded: chain B residue 511 THR Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 565 LEU Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 630 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 650 VAL Chi-restraints excluded: chain B residue 665 LEU 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 707 ILE Chi-restraints excluded: chain B residue 708 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 94 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 119 optimal weight: 0.0670 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 HIS B 235 GLN B 542 ASN B 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.139086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115528 restraints weight = 12994.352| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.24 r_work: 0.3162 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10242 Z= 0.149 Angle : 0.628 14.096 13910 Z= 0.305 Chirality : 0.043 0.173 1596 Planarity : 0.004 0.041 1730 Dihedral : 6.468 88.914 1430 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.16 % Allowed : 31.49 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1262 helix: -0.62 (0.21), residues: 630 sheet: -2.43 (0.61), residues: 66 loop : -2.26 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 167 HIS 0.003 0.001 HIS A 240 PHE 0.026 0.001 PHE A 789 TYR 0.017 0.001 TYR A 736 ARG 0.004 0.000 ARG A 432 Details of bonding type rmsd hydrogen bonds : bond 0.04104 ( 345) hydrogen bonds : angle 4.37291 ( 999) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.67207 ( 4) covalent geometry : bond 0.00364 (10240) covalent geometry : angle 0.62820 (13906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4067.59 seconds wall clock time: 71 minutes 33.33 seconds (4293.33 seconds total)