Starting phenix.real_space_refine on Wed Mar 4 17:46:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.map" model { file = "/net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epc_31237/03_2026/7epc_31237.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5016 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 7072 2.51 5 N 1958 2.21 5 O 2111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11216 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5585 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 37, 'TRANS': 744} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 614 Unresolved non-hydrogen angles: 779 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 13, 'ARG:plan': 9, 'GLN:plan1': 10, 'ASN:plan1': 7, 'TYR:plan': 9, 'PHE:plan': 8, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 335 Chain: "B" Number of atoms: 5631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5631 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 147} Link IDs: {'PTRANS': 37, 'TRANS': 744} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 720 Unresolved non-hydrogen dihedrals: 466 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'ASP:plan': 13, 'TYR:plan': 9, 'GLU:plan': 11, 'ARG:plan': 9, 'GLN:plan1': 9, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 9} Unresolved non-hydrogen planarities: 306 Time building chain proxies: 3.05, per 1000 atoms: 0.27 Number of scatterers: 11216 At special positions: 0 Unit cell: (110.4, 95.2, 195.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 2111 8.00 N 1958 7.00 C 7072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 548 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 560 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 749 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 604.1 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 46.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 76 through 92 Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.502A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.285A pdb=" N LEU A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 217 removed outlier: 4.016A pdb=" N GLN A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 246 Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 344 through 351 removed outlier: 3.656A pdb=" N ALA A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 407 through 430 Processing helix chain 'A' and resid 437 through 443 removed outlier: 4.375A pdb=" N GLU A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 442 " --> pdb=" O PRO A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 591 through 609 removed outlier: 3.885A pdb=" N PHE A 607 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 613 removed outlier: 3.996A pdb=" N ILE A 613 " --> pdb=" O ALA A 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 610 through 613' Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.877A pdb=" N ALA A 623 " --> pdb=" O ILE A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 648 removed outlier: 3.538A pdb=" N PHE A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE A 644 " --> pdb=" O TYR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 664 removed outlier: 3.898A pdb=" N VAL A 660 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE A 661 " --> pdb=" O PHE A 657 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 662 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 686 removed outlier: 3.733A pdb=" N ILE A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 672 " --> pdb=" O ILE A 668 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A 683 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 724 removed outlier: 3.826A pdb=" N LEU A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 706 " --> pdb=" O GLN A 702 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 721 " --> pdb=" O VAL A 717 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 722 " --> pdb=" O PHE A 718 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 724 " --> pdb=" O TRP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 772 removed outlier: 4.416A pdb=" N SER A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 769 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 772 " --> pdb=" O VAL A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 775 No H-bonds generated for 'chain 'A' and resid 773 through 775' Processing helix chain 'A' and resid 783 through 809 removed outlier: 3.519A pdb=" N PHE A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR A 793 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 794 " --> pdb=" O ILE A 790 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 795 " --> pdb=" O GLY A 791 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 796 " --> pdb=" O PHE A 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 805 " --> pdb=" O TRP A 801 " (cutoff:3.500A) Proline residue: A 806 - end of helix removed outlier: 4.079A pdb=" N PHE A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 841 removed outlier: 3.549A pdb=" N VAL A 835 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'B' and resid 76 through 92 Processing helix chain 'B' and resid 111 through 128 removed outlier: 4.009A pdb=" N ALA B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU B 126 " --> pdb=" O PHE B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 removed outlier: 4.251A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 4.012A pdb=" N GLN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 246 Processing helix chain 'B' and resid 265 through 275 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.657A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 407 through 430 Processing helix chain 'B' and resid 437 through 443 removed outlier: 4.354A pdb=" N GLU B 441 " --> pdb=" O CYS B 437 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 removed outlier: 3.581A pdb=" N LEU B 449 " --> pdb=" O GLY B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 514 removed outlier: 4.301A pdb=" N LYS B 513 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 609 removed outlier: 3.643A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 613 removed outlier: 4.002A pdb=" N ILE B 613 " --> pdb=" O ALA B 610 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 610 through 613' Processing helix chain 'B' and resid 620 through 624 removed outlier: 3.868A pdb=" N ALA B 623 " --> pdb=" O ILE B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 648 removed outlier: 3.519A pdb=" N PHE B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE B 644 " --> pdb=" O TYR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 664 removed outlier: 3.996A pdb=" N VAL B 660 " --> pdb=" O SER B 656 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE B 661 " --> pdb=" O PHE B 657 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 662 " --> pdb=" O ARG B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 686 removed outlier: 3.671A pdb=" N TYR B 670 " --> pdb=" O MET B 666 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 683 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 724 removed outlier: 3.544A pdb=" N LEU B 703 " --> pdb=" O PRO B 699 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 706 " --> pdb=" O GLN B 702 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 709 " --> pdb=" O ILE B 705 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 717 " --> pdb=" O GLN B 713 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TRP B 720 " --> pdb=" O GLY B 716 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE B 722 " --> pdb=" O PHE B 718 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 724 " --> pdb=" O TRP B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 778 removed outlier: 3.689A pdb=" N ILE B 756 " --> pdb=" O THR B 752 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 765 " --> pdb=" O GLY B 761 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 766 " --> pdb=" O TYR B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 809 removed outlier: 3.635A pdb=" N PHE B 792 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 793 " --> pdb=" O TYR B 789 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET B 794 " --> pdb=" O ILE B 790 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR B 795 " --> pdb=" O GLY B 791 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 797 " --> pdb=" O THR B 793 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N CYS B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE B 799 " --> pdb=" O TYR B 795 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL B 800 " --> pdb=" O THR B 796 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 805 " --> pdb=" O TRP B 801 " (cutoff:3.500A) Proline residue: B 806 - end of helix Processing helix chain 'B' and resid 819 through 850 removed outlier: 4.039A pdb=" N THR B 823 " --> pdb=" O TYR B 819 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) Proline residue: B 843 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 7.000A pdb=" N LEU A 51 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 50 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY A 152 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N ILE A 177 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 153 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.610A pdb=" N VAL A 254 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 225 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER A 222 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 336 " --> pdb=" O GLY A 312 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 337 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 478 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 496 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLN A 481 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU A 494 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 removed outlier: 3.923A pdb=" N PHE A 457 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.944A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR B 50 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY B 152 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE B 177 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 153 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 249 through 255 removed outlier: 6.813A pdb=" N VAL B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN B 252 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 254 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 225 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR B 220 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL B 284 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER B 222 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 283 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 337 " --> pdb=" O ASP B 478 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B 478 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN B 481 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LEU B 494 " --> pdb=" O GLN B 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 457 through 458 removed outlier: 3.913A pdb=" N PHE B 457 " --> pdb=" O VAL B 465 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3778 1.35 - 1.47: 2695 1.47 - 1.59: 4868 1.59 - 1.71: 0 1.71 - 1.83: 104 Bond restraints: 11445 Sorted by residual: bond pdb=" C ILE B 518 " pdb=" N PRO B 519 " ideal model delta sigma weight residual 1.333 1.355 -0.022 1.20e-02 6.94e+03 3.49e+00 bond pdb=" C ILE A 805 " pdb=" N PRO A 806 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.08e-02 8.57e+03 3.37e+00 bond pdb=" C VAL A 522 " pdb=" O VAL A 522 " ideal model delta sigma weight residual 1.232 1.243 -0.011 1.30e-02 5.92e+03 7.47e-01 bond pdb=" CA CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.89e-01 bond pdb=" N PRO A 781 " pdb=" CA PRO A 781 " ideal model delta sigma weight residual 1.469 1.475 -0.006 7.40e-03 1.83e+04 6.58e-01 ... (remaining 11440 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 15218 1.37 - 2.73: 331 2.73 - 4.10: 49 4.10 - 5.46: 22 5.46 - 6.83: 5 Bond angle restraints: 15625 Sorted by residual: angle pdb=" C VAL B 522 " pdb=" N CYS B 523 " pdb=" CA CYS B 523 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N ILE A 606 " pdb=" CA ILE A 606 " pdb=" C ILE A 606 " ideal model delta sigma weight residual 112.98 109.14 3.84 1.25e+00 6.40e-01 9.41e+00 angle pdb=" N ILE B 606 " pdb=" CA ILE B 606 " pdb=" C ILE B 606 " ideal model delta sigma weight residual 112.98 109.16 3.82 1.25e+00 6.40e-01 9.34e+00 angle pdb=" C VAL A 522 " pdb=" N CYS A 523 " pdb=" CA CYS A 523 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.30e+00 angle pdb=" N THR B 811 " pdb=" CA THR B 811 " pdb=" C THR B 811 " ideal model delta sigma weight residual 114.56 110.75 3.81 1.27e+00 6.20e-01 9.00e+00 ... (remaining 15620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6402 17.99 - 35.97: 360 35.97 - 53.95: 59 53.95 - 71.94: 11 71.94 - 89.92: 7 Dihedral angle restraints: 6839 sinusoidal: 2317 harmonic: 4522 Sorted by residual: dihedral pdb=" CB CYS A 527 " pdb=" SG CYS A 527 " pdb=" SG CYS A 545 " pdb=" CB CYS A 545 " ideal model delta sinusoidal sigma weight residual -86.00 -170.47 84.47 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A 523 " pdb=" SG CYS A 523 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 21.82 71.18 1 1.00e+01 1.00e-02 6.50e+01 dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -150.73 64.73 1 1.00e+01 1.00e-02 5.50e+01 ... (remaining 6836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1199 0.030 - 0.060: 411 0.060 - 0.090: 126 0.090 - 0.120: 70 0.120 - 0.149: 2 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CA VAL A 145 " pdb=" N VAL A 145 " pdb=" C VAL A 145 " pdb=" CB VAL A 145 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA VAL B 145 " pdb=" N VAL B 145 " pdb=" C VAL B 145 " pdb=" CB VAL B 145 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE A 154 " pdb=" N ILE A 154 " pdb=" C ILE A 154 " pdb=" CB ILE A 154 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 1805 not shown) Planarity restraints: 2051 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 805 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO B 806 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 806 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 806 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 805 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 806 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 806 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 806 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 842 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO B 843 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 843 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 843 " -0.016 5.00e-02 4.00e+02 ... (remaining 2048 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3505 2.82 - 3.34: 10209 3.34 - 3.86: 17002 3.86 - 4.38: 18075 4.38 - 4.90: 31893 Nonbonded interactions: 80684 Sorted by model distance: nonbonded pdb=" O ILE A 807 " pdb=" OG1 THR A 811 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLN A 205 " pdb=" OG SER A 313 " model vdw 2.322 3.040 nonbonded pdb=" O ILE A 705 " pdb=" OG SER A 708 " model vdw 2.333 3.040 nonbonded pdb=" O MET B 666 " pdb=" OG SER B 669 " model vdw 2.339 3.040 nonbonded pdb=" OG SER B 698 " pdb=" OG SER B 701 " model vdw 2.339 3.040 ... (remaining 80679 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 219 or (resid 220 and (name N or name CA or nam \ e C or name O or name CB )) or resid 221 through 242 or (resid 243 and (name N o \ r name CA or name C or name O or name CB )) or resid 244 through 265 or (resid 2 \ 66 and (name N or name CA or name C or name O or name CB )) or resid 267 through \ 271 or (resid 272 and (name N or name CA or name C or name O or name CB )) or r \ esid 273 through 319 or (resid 320 through 321 and (name N or name CA or name C \ or name O or name CB )) or resid 322 through 355 or (resid 356 and (name N or na \ me CA or name C or name O or name CB )) or resid 357 through 402 or (resid 403 a \ nd (name N or name CA or name C or name O or name CB )) or resid 404 through 625 \ or (resid 626 through 627 and (name N or name CA or name C or name O or name CB \ )) or resid 628 through 643 or (resid 644 through 645 and (name N or name CA or \ name C or name O or name CB )) or resid 646 through 673 or (resid 674 and (name \ N or name CA or name C or name O or name CB )) or resid 675 through 701 or (res \ id 702 and (name N or name CA or name C or name O or name CB )) or resid 703 thr \ ough 717 or (resid 718 and (name N or name CA or name C or name O or name CB )) \ or resid 719 through 826 or (resid 827 and (name N or name CA or name C or name \ O or name CB )) or resid 828 through 850)) selection = (chain 'B' and (resid 41 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 72 or (resid 73 and (name N or nam \ e CA or name C or name O or name CB )) or resid 74 through 147 or (resid 148 and \ (name N or name CA or name C or name O or name CB )) or resid 149 through 258 o \ r (resid 259 through 262 and (name N or name CA or name C or name O or name CB ) \ ) or resid 263 through 302 or (resid 303 and (name N or name CA or name C or nam \ e O or name CB )) or resid 304 through 374 or (resid 375 and (name N or name CA \ or name C or name O or name CB )) or resid 376 through 394 or (resid 395 and (na \ me N or name CA or name C or name O or name CB )) or resid 396 through 397 or (r \ esid 398 and (name N or name CA or name C or name O or name CB )) or resid 399 t \ hrough 400 or (resid 401 and (name N or name CA or name C or name O or name CB ) \ ) or resid 402 through 432 or (resid 433 through 434 and (name N or name CA or n \ ame C or name O or name CB )) or resid 435 through 441 or (resid 442 through 443 \ and (name N or name CA or name C or name O or name CB )) or resid 444 through 4 \ 46 or (resid 447 and (name N or name CA or name C or name O or name CB )) or res \ id 448 through 516 or (resid 517 through 518 and (name N or name CA or name C or \ name O or name CB )) or resid 519 through 524 or (resid 525 and (name N or name \ CA or name C or name O or name CB )) or resid 526 through 554 or (resid 555 thr \ ough 556 and (name N or name CA or name C or name O or name CB )) or resid 557 o \ r (resid 558 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 59 through 570 or (resid 571 and (name N or name CA or name C or name O or name \ CB )) or resid 572 through 585 or (resid 586 through 589 and (name N or name CA \ or name C or name O or name CB )) or resid 590 through 661 or (resid 662 and (na \ me N or name CA or name C or name O or name CB )) or resid 663 through 727 or (r \ esid 728 through 739 and (name N or name CA or name C or name O or name CB )) or \ resid 740 through 747 or (resid 748 and (name N or name CA or name C or name O \ or name CB )) or resid 749 through 763 or (resid 764 through 765 and (name N or \ name CA or name C or name O or name CB )) or resid 766 through 812 or (resid 813 \ and (name N or name CA or name C or name O or name CB )) or resid 814 through 8 \ 29 or (resid 830 through 831 and (name N or name CA or name C or name O or name \ CB )) or resid 832 through 850)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.030 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4809 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 : 0.002 0.031 11464 Z= 0.100 Angle : 0.503 6.830 15663 Z= 0.294 Chirality : 0.038 0.149 1808 Planarity : 0.003 0.045 2051 Dihedral : 11.278 89.924 3862 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.17), residues: 1548 helix: -1.56 (0.16), residues: 662 sheet: -0.91 (0.45), residues: 128 loop : -2.56 (0.18), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 453 TYR 0.003 0.000 TYR A 220 PHE 0.010 0.000 PHE A 808 TRP 0.006 0.001 TRP A 543 HIS 0.001 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00179 (11445) covalent geometry : angle 0.50103 (15625) SS BOND : bond 0.00111 ( 19) SS BOND : angle 0.93142 ( 38) hydrogen bonds : bond 0.24572 ( 475) hydrogen bonds : angle 6.46047 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 VAL cc_start: 0.4986 (m) cc_final: 0.4057 (p) REVERT: A 801 TRP cc_start: 0.6167 (m100) cc_final: 0.5803 (m-10) REVERT: B 161 VAL cc_start: 0.5140 (m) cc_final: 0.4244 (p) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.0993 time to fit residues: 42.1981 Evaluate side-chains 204 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 273 GLN A 325 GLN A 357 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 567 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.147316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.131134 restraints weight = 26506.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130285 restraints weight = 57732.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.130868 restraints weight = 48048.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130883 restraints weight = 33354.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131167 restraints weight = 36791.065| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11464 Z= 0.147 Angle : 0.626 10.187 15663 Z= 0.313 Chirality : 0.043 0.178 1808 Planarity : 0.004 0.038 2051 Dihedral : 3.270 15.259 1662 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.96 % Allowed : 11.57 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.19), residues: 1548 helix: 0.13 (0.19), residues: 652 sheet: -0.86 (0.45), residues: 126 loop : -2.26 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 104 TYR 0.023 0.002 TYR A 681 PHE 0.024 0.002 PHE B 775 TRP 0.018 0.002 TRP B 368 HIS 0.010 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00332 (11445) covalent geometry : angle 0.62545 (15625) SS BOND : bond 0.00316 ( 19) SS BOND : angle 0.78105 ( 38) hydrogen bonds : bond 0.04057 ( 475) hydrogen bonds : angle 4.10363 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5041 (mttt) REVERT: A 162 SER cc_start: 0.5605 (m) cc_final: 0.5268 (m) REVERT: A 674 LEU cc_start: 0.6061 (tp) cc_final: 0.5817 (tp) REVERT: A 773 TYR cc_start: 0.4370 (m-10) cc_final: 0.4127 (m-10) REVERT: B 41 HIS cc_start: 0.5822 (m-70) cc_final: 0.5512 (m-70) REVERT: B 412 ILE cc_start: 0.5604 (mt) cc_final: 0.4558 (tp) REVERT: B 542 CYS cc_start: 0.4368 (OUTLIER) cc_final: 0.4128 (p) outliers start: 31 outliers final: 14 residues processed: 220 average time/residue: 0.1004 time to fit residues: 31.8000 Evaluate side-chains 187 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 706 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.0040 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.0030 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.146577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.124969 restraints weight = 26672.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.124742 restraints weight = 53814.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.125556 restraints weight = 43710.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.127278 restraints weight = 28124.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.127540 restraints weight = 19626.977| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11464 Z= 0.116 Angle : 0.556 10.360 15663 Z= 0.277 Chirality : 0.041 0.162 1808 Planarity : 0.004 0.035 2051 Dihedral : 3.131 13.439 1662 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.49 % Allowed : 15.11 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1548 helix: 0.96 (0.20), residues: 640 sheet: -0.75 (0.53), residues: 104 loop : -2.05 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 269 TYR 0.013 0.001 TYR B 433 PHE 0.020 0.001 PHE A 346 TRP 0.020 0.001 TRP A 310 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00256 (11445) covalent geometry : angle 0.55555 (15625) SS BOND : bond 0.00154 ( 19) SS BOND : angle 0.78143 ( 38) hydrogen bonds : bond 0.03682 ( 475) hydrogen bonds : angle 3.70104 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 LEU cc_start: 0.6190 (tp) cc_final: 0.5946 (tp) REVERT: A 773 TYR cc_start: 0.4598 (m-10) cc_final: 0.4292 (m-10) REVERT: A 801 TRP cc_start: 0.5638 (m100) cc_final: 0.5304 (m100) REVERT: A 826 THR cc_start: 0.7889 (m) cc_final: 0.7678 (p) REVERT: B 489 ASN cc_start: 0.7232 (m-40) cc_final: 0.6983 (m-40) REVERT: B 562 HIS cc_start: 0.6899 (t-90) cc_final: 0.6688 (t-90) outliers start: 26 outliers final: 17 residues processed: 190 average time/residue: 0.0822 time to fit residues: 23.5983 Evaluate side-chains 175 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 149 optimal weight: 0.0670 chunk 45 optimal weight: 0.3980 chunk 104 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 28 optimal weight: 0.0570 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 94 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 325 GLN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.146460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.124533 restraints weight = 26890.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.124629 restraints weight = 50584.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.125300 restraints weight = 45446.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.126887 restraints weight = 28727.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127123 restraints weight = 19403.905| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5709 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11464 Z= 0.109 Angle : 0.535 8.199 15663 Z= 0.264 Chirality : 0.040 0.127 1808 Planarity : 0.003 0.036 2051 Dihedral : 3.086 13.195 1662 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 16.06 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1548 helix: 1.18 (0.20), residues: 652 sheet: -0.64 (0.54), residues: 104 loop : -1.98 (0.19), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 191 TYR 0.019 0.001 TYR B 433 PHE 0.028 0.001 PHE A 346 TRP 0.016 0.001 TRP B 368 HIS 0.012 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00244 (11445) covalent geometry : angle 0.53401 (15625) SS BOND : bond 0.00181 ( 19) SS BOND : angle 0.77677 ( 38) hydrogen bonds : bond 0.03079 ( 475) hydrogen bonds : angle 3.53981 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7489 (pp20) cc_final: 0.7194 (pt0) REVERT: A 355 LEU cc_start: 0.8006 (mt) cc_final: 0.7588 (mp) REVERT: A 465 VAL cc_start: 0.4413 (m) cc_final: 0.3348 (t) REVERT: A 801 TRP cc_start: 0.5564 (m100) cc_final: 0.5182 (m100) REVERT: B 489 ASN cc_start: 0.7102 (m-40) cc_final: 0.6878 (m-40) REVERT: B 542 CYS cc_start: 0.4272 (OUTLIER) cc_final: 0.4063 (p) outliers start: 30 outliers final: 18 residues processed: 173 average time/residue: 0.0833 time to fit residues: 22.2126 Evaluate side-chains 172 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 0.0070 chunk 79 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 chunk 127 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 567 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 219 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.144262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.122384 restraints weight = 26424.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.121722 restraints weight = 42750.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119328 restraints weight = 34948.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.119149 restraints weight = 37300.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.118818 restraints weight = 30172.539| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.6593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 11464 Z= 0.163 Angle : 0.605 8.388 15663 Z= 0.311 Chirality : 0.043 0.199 1808 Planarity : 0.004 0.054 2051 Dihedral : 3.482 15.015 1662 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.44 % Allowed : 16.92 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.20), residues: 1548 helix: 0.78 (0.20), residues: 682 sheet: -0.54 (0.48), residues: 126 loop : -2.06 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 679 TYR 0.023 0.002 TYR A 416 PHE 0.022 0.002 PHE A 346 TRP 0.042 0.002 TRP A 368 HIS 0.012 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00374 (11445) covalent geometry : angle 0.60345 (15625) SS BOND : bond 0.00401 ( 19) SS BOND : angle 0.99892 ( 38) hydrogen bonds : bond 0.03747 ( 475) hydrogen bonds : angle 3.75711 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 PHE cc_start: 0.6070 (t80) cc_final: 0.5725 (t80) REVERT: B 48 ASP cc_start: 0.7077 (p0) cc_final: 0.6586 (p0) REVERT: B 147 PRO cc_start: 0.7218 (Cg_exo) cc_final: 0.6984 (Cg_endo) REVERT: B 489 ASN cc_start: 0.7459 (m-40) cc_final: 0.7180 (m-40) REVERT: B 542 CYS cc_start: 0.4651 (OUTLIER) cc_final: 0.4439 (p) REVERT: B 607 PHE cc_start: 0.6150 (OUTLIER) cc_final: 0.5278 (t80) outliers start: 36 outliers final: 18 residues processed: 181 average time/residue: 0.0807 time to fit residues: 22.4486 Evaluate side-chains 162 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 717 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 820 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 128 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 0.0570 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 326 HIS ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 HIS B 58 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.142197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.121014 restraints weight = 26611.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.117097 restraints weight = 39381.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.115183 restraints weight = 37315.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.114870 restraints weight = 38823.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114427 restraints weight = 31899.431| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11464 Z= 0.154 Angle : 0.618 10.582 15663 Z= 0.308 Chirality : 0.043 0.154 1808 Planarity : 0.004 0.036 2051 Dihedral : 3.515 14.619 1662 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.35 % Allowed : 19.69 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.21), residues: 1548 helix: 0.93 (0.20), residues: 684 sheet: -0.46 (0.49), residues: 126 loop : -1.99 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 269 TYR 0.014 0.001 TYR A 819 PHE 0.027 0.002 PHE A 804 TRP 0.020 0.002 TRP B 511 HIS 0.007 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00371 (11445) covalent geometry : angle 0.61674 (15625) SS BOND : bond 0.00283 ( 19) SS BOND : angle 0.92204 ( 38) hydrogen bonds : bond 0.03604 ( 475) hydrogen bonds : angle 3.71674 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6124 (mptt) cc_final: 0.5827 (mmtm) REVERT: A 193 ASP cc_start: 0.7886 (t0) cc_final: 0.7588 (m-30) REVERT: B 48 ASP cc_start: 0.7188 (p0) cc_final: 0.6591 (p0) REVERT: B 493 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7075 (mtm110) REVERT: B 511 TRP cc_start: 0.6562 (p90) cc_final: 0.6273 (p90) REVERT: B 542 CYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4474 (p) REVERT: B 607 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5610 (t80) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.0838 time to fit residues: 19.5869 Evaluate side-chains 143 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 0.2980 chunk 23 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.140699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.115952 restraints weight = 26332.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111652 restraints weight = 44253.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109356 restraints weight = 40557.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.108946 restraints weight = 37518.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.109705 restraints weight = 32181.240| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11464 Z= 0.154 Angle : 0.606 10.316 15663 Z= 0.301 Chirality : 0.042 0.170 1808 Planarity : 0.004 0.043 2051 Dihedral : 3.562 14.495 1662 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.20 % Allowed : 21.80 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.21), residues: 1548 helix: 1.01 (0.20), residues: 676 sheet: -0.50 (0.47), residues: 138 loop : -1.97 (0.20), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 269 TYR 0.026 0.001 TYR B 433 PHE 0.017 0.001 PHE A 346 TRP 0.016 0.002 TRP B 543 HIS 0.008 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00368 (11445) covalent geometry : angle 0.60454 (15625) SS BOND : bond 0.00188 ( 19) SS BOND : angle 0.92381 ( 38) hydrogen bonds : bond 0.03655 ( 475) hydrogen bonds : angle 3.68145 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7912 (t0) cc_final: 0.7619 (m-30) REVERT: A 387 ASP cc_start: 0.5904 (t0) cc_final: 0.5589 (t0) REVERT: A 801 TRP cc_start: 0.6588 (m100) cc_final: 0.5902 (m-10) REVERT: B 48 ASP cc_start: 0.7490 (p0) cc_final: 0.6902 (p0) REVERT: B 607 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.5848 (t80) outliers start: 23 outliers final: 14 residues processed: 145 average time/residue: 0.0914 time to fit residues: 19.4153 Evaluate side-chains 132 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 67 optimal weight: 0.0040 chunk 100 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 0.0370 chunk 111 optimal weight: 5.9990 overall best weight: 0.3870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 357 ASN B 404 GLN B 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.142312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.117480 restraints weight = 25988.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.112212 restraints weight = 37904.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108948 restraints weight = 37126.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.109026 restraints weight = 37726.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109537 restraints weight = 33451.566| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.8789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11464 Z= 0.108 Angle : 0.576 13.302 15663 Z= 0.280 Chirality : 0.041 0.147 1808 Planarity : 0.004 0.050 2051 Dihedral : 3.419 13.937 1662 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.63 % Allowed : 21.89 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1548 helix: 1.14 (0.20), residues: 676 sheet: -0.17 (0.49), residues: 130 loop : -1.99 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 269 TYR 0.019 0.001 TYR B 433 PHE 0.029 0.001 PHE B 684 TRP 0.022 0.001 TRP B 368 HIS 0.014 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00249 (11445) covalent geometry : angle 0.57506 (15625) SS BOND : bond 0.00159 ( 19) SS BOND : angle 0.85355 ( 38) hydrogen bonds : bond 0.03086 ( 475) hydrogen bonds : angle 3.55878 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.5899 (t0) cc_final: 0.5652 (t0) REVERT: A 801 TRP cc_start: 0.6764 (m100) cc_final: 0.6038 (m-10) REVERT: B 48 ASP cc_start: 0.7420 (p0) cc_final: 0.6840 (p0) REVERT: B 88 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6636 (pp30) REVERT: B 607 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.5973 (t80) outliers start: 17 outliers final: 14 residues processed: 130 average time/residue: 0.0820 time to fit residues: 16.5818 Evaluate side-chains 131 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 124 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 49 optimal weight: 0.0570 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.136839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.111930 restraints weight = 24905.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110318 restraints weight = 39441.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.107755 restraints weight = 32207.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107202 restraints weight = 33445.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106462 restraints weight = 29545.319| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.9071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11464 Z= 0.121 Angle : 0.593 11.188 15663 Z= 0.289 Chirality : 0.041 0.202 1808 Planarity : 0.004 0.050 2051 Dihedral : 3.426 14.750 1662 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.10 % Allowed : 21.51 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.21), residues: 1548 helix: 1.12 (0.20), residues: 682 sheet: -0.44 (0.47), residues: 138 loop : -1.96 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 269 TYR 0.018 0.001 TYR B 433 PHE 0.026 0.001 PHE B 684 TRP 0.021 0.001 TRP B 511 HIS 0.011 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00288 (11445) covalent geometry : angle 0.59187 (15625) SS BOND : bond 0.00139 ( 19) SS BOND : angle 0.88968 ( 38) hydrogen bonds : bond 0.03237 ( 475) hydrogen bonds : angle 3.57185 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.5993 (t0) cc_final: 0.5735 (t0) REVERT: A 766 LEU cc_start: 0.5005 (pp) cc_final: 0.4287 (mp) REVERT: A 801 TRP cc_start: 0.6583 (m100) cc_final: 0.5959 (m-10) REVERT: B 48 ASP cc_start: 0.7589 (p0) cc_final: 0.7051 (p0) REVERT: B 88 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.7225 (pp30) REVERT: B 440 MET cc_start: 0.7979 (ttp) cc_final: 0.7651 (ttp) REVERT: B 607 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.5975 (t80) outliers start: 22 outliers final: 19 residues processed: 135 average time/residue: 0.0916 time to fit residues: 18.7086 Evaluate side-chains 135 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 118 GLN B 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.109506 restraints weight = 25038.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.107427 restraints weight = 36963.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.105368 restraints weight = 32266.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104055 restraints weight = 36135.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103037 restraints weight = 36810.715| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.9669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11464 Z= 0.192 Angle : 0.663 11.478 15663 Z= 0.329 Chirality : 0.044 0.268 1808 Planarity : 0.004 0.058 2051 Dihedral : 3.755 19.379 1662 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.20 % Allowed : 21.51 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.21), residues: 1548 helix: 1.05 (0.20), residues: 686 sheet: -0.53 (0.48), residues: 138 loop : -1.92 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 269 TYR 0.017 0.001 TYR B 433 PHE 0.027 0.002 PHE A 804 TRP 0.019 0.002 TRP B 368 HIS 0.005 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00471 (11445) covalent geometry : angle 0.66156 (15625) SS BOND : bond 0.00182 ( 19) SS BOND : angle 1.00928 ( 38) hydrogen bonds : bond 0.04155 ( 475) hydrogen bonds : angle 3.84474 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 ASP cc_start: 0.6143 (t0) cc_final: 0.5887 (t0) REVERT: A 801 TRP cc_start: 0.6576 (m100) cc_final: 0.5966 (m-10) REVERT: B 48 ASP cc_start: 0.7736 (p0) cc_final: 0.7227 (p0) REVERT: B 325 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6829 (tp40) REVERT: B 440 MET cc_start: 0.8005 (ttp) cc_final: 0.7670 (ttp) REVERT: B 562 HIS cc_start: 0.7705 (t-90) cc_final: 0.7446 (t-90) REVERT: B 607 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.6003 (t80) REVERT: B 767 MET cc_start: 0.6339 (ttt) cc_final: 0.6088 (ttm) outliers start: 23 outliers final: 17 residues processed: 133 average time/residue: 0.0924 time to fit residues: 18.5385 Evaluate side-chains 125 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 104 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 326 HIS A 470 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.136350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.111174 restraints weight = 25385.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.106238 restraints weight = 42842.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103950 restraints weight = 35468.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.103197 restraints weight = 34436.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103274 restraints weight = 32368.498| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.9836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11464 Z= 0.119 Angle : 0.611 10.909 15663 Z= 0.297 Chirality : 0.042 0.166 1808 Planarity : 0.004 0.059 2051 Dihedral : 3.558 15.941 1662 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.82 % Allowed : 23.04 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.21), residues: 1548 helix: 1.23 (0.20), residues: 670 sheet: -0.46 (0.48), residues: 138 loop : -2.00 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 269 TYR 0.017 0.001 TYR B 402 PHE 0.027 0.001 PHE A 684 TRP 0.017 0.001 TRP A 363 HIS 0.013 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00283 (11445) covalent geometry : angle 0.60966 (15625) SS BOND : bond 0.00164 ( 19) SS BOND : angle 0.92158 ( 38) hydrogen bonds : bond 0.03305 ( 475) hydrogen bonds : angle 3.67525 ( 1395) =============================================================================== Job complete usr+sys time: 1757.71 seconds wall clock time: 30 minutes 58.08 seconds (1858.08 seconds total)