Starting phenix.real_space_refine on Tue Dec 31 08:49:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epc_31237/12_2024/7epc_31237.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epc_31237/12_2024/7epc_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_31237/12_2024/7epc_31237.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epc_31237/12_2024/7epc_31237.map" model { file = "/net/cci-nas-00/data/ceres_data/7epc_31237/12_2024/7epc_31237.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epc_31237/12_2024/7epc_31237.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 15, 'ARG:plan': 9} 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: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 11, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 306 Time building chain proxies: 7.31, per 1000 atoms: 0.65 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: 2.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.22 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: 3.36 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.440 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- 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 11445 Z= 0.120 Angle : 0.501 6.830 15625 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (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 TRP 0.006 0.001 TRP A 543 HIS 0.001 0.000 HIS A 326 PHE 0.010 0.000 PHE A 808 TYR 0.003 0.000 TYR A 220 ARG 0.001 0.000 ARG A 453 *********************** 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 : 1.394 Fit side-chains 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: 0.4058 (p) REVERT: A 801 TRP cc_start: 0.6167 (m100) cc_final: 0.5809 (m-10) REVERT: B 161 VAL cc_start: 0.5140 (m) cc_final: 0.4238 (p) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2318 time to fit residues: 97.5563 Evaluate side-chains 203 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.0270 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 91 optimal weight: 0.5980 chunk 141 optimal weight: 9.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 325 GLN A 357 ASN ** A 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11445 Z= 0.248 Angle : 0.660 11.213 15625 Z= 0.333 Chirality : 0.043 0.148 1808 Planarity : 0.004 0.040 2051 Dihedral : 3.485 16.316 1662 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.96 % Allowed : 12.05 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.19), residues: 1548 helix: -0.06 (0.19), residues: 646 sheet: -1.11 (0.50), residues: 104 loop : -2.16 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 368 HIS 0.008 0.001 HIS A 326 PHE 0.036 0.002 PHE B 721 TYR 0.013 0.001 TYR B 551 ARG 0.005 0.000 ARG B 476 *********************** 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 227 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.5849 (OUTLIER) cc_final: 0.4931 (mttt) REVERT: A 235 VAL cc_start: 0.7806 (t) cc_final: 0.7279 (m) REVERT: A 773 TYR cc_start: 0.5311 (m-10) cc_final: 0.5019 (m-10) REVERT: A 801 TRP cc_start: 0.5802 (m100) cc_final: 0.5109 (m100) REVERT: B 41 HIS cc_start: 0.6254 (m-70) cc_final: 0.5979 (m-70) REVERT: B 542 CYS cc_start: 0.5070 (OUTLIER) cc_final: 0.4865 (p) REVERT: B 562 HIS cc_start: 0.7243 (t-90) cc_final: 0.6902 (t-90) outliers start: 31 outliers final: 15 residues processed: 215 average time/residue: 0.2365 time to fit residues: 74.0697 Evaluate side-chains 177 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 160 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 662 LEU 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 78 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 GLN A 483 GLN A 562 HIS ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11445 Z= 0.234 Angle : 0.592 10.317 15625 Z= 0.302 Chirality : 0.043 0.266 1808 Planarity : 0.004 0.037 2051 Dihedral : 3.407 15.995 1662 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.44 % Allowed : 15.11 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1548 helix: 0.64 (0.20), residues: 666 sheet: -0.67 (0.48), residues: 126 loop : -2.15 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 310 HIS 0.005 0.001 HIS A 326 PHE 0.020 0.002 PHE A 346 TYR 0.022 0.001 TYR A 416 ARG 0.009 0.001 ARG B 255 *********************** 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 208 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.7368 (mt) cc_final: 0.7047 (mt) REVERT: A 415 VAL cc_start: 0.7895 (t) cc_final: 0.6041 (m) REVERT: A 773 TYR cc_start: 0.5415 (m-10) cc_final: 0.5129 (m-10) REVERT: A 826 THR cc_start: 0.8314 (m) cc_final: 0.7963 (p) REVERT: B 253 SER cc_start: 0.6548 (m) cc_final: 0.6331 (p) REVERT: B 480 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7249 (m-10) REVERT: B 794 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6892 (tpp) outliers start: 36 outliers final: 19 residues processed: 196 average time/residue: 0.2193 time to fit residues: 62.8961 Evaluate side-chains 163 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 541 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 114 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER 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 480 PHE Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 798 CYS 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 140 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.8430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11445 Z= 0.457 Angle : 0.767 13.203 15625 Z= 0.396 Chirality : 0.048 0.376 1808 Planarity : 0.005 0.045 2051 Dihedral : 4.365 23.885 1662 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.16 % Allowed : 17.78 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1548 helix: 0.35 (0.19), residues: 674 sheet: -1.31 (0.46), residues: 130 loop : -2.22 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 368 HIS 0.010 0.002 HIS A 326 PHE 0.036 0.003 PHE A 194 TYR 0.022 0.002 TYR B 433 ARG 0.014 0.001 ARG B 78 *********************** 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 191 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 137 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6548 (mptt) cc_final: 0.6142 (mmtm) REVERT: A 272 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8332 (mmtp) REVERT: A 387 ASP cc_start: 0.6236 (t0) cc_final: 0.5941 (t0) REVERT: B 48 ASP cc_start: 0.7610 (p0) cc_final: 0.7190 (p0) REVERT: B 118 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7480 (mm-40) REVERT: B 286 PHE cc_start: 0.8723 (m-80) cc_final: 0.8486 (m-80) REVERT: B 436 VAL cc_start: 0.3765 (OUTLIER) cc_final: 0.2189 (p) REVERT: B 493 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.7242 (mtm110) REVERT: B 555 PHE cc_start: 0.7529 (m-80) cc_final: 0.7153 (m-80) outliers start: 54 outliers final: 33 residues processed: 179 average time/residue: 0.2224 time to fit residues: 58.4312 Evaluate side-chains 150 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 646 MET Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 770 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 368 TRP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 777 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 Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 HIS ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.9448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 11445 Z= 0.405 Angle : 0.677 10.728 15625 Z= 0.347 Chirality : 0.045 0.241 1808 Planarity : 0.005 0.054 2051 Dihedral : 4.106 24.103 1662 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.40 % Allowed : 21.32 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1548 helix: 0.74 (0.20), residues: 682 sheet: -1.32 (0.44), residues: 144 loop : -2.05 (0.20), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 368 HIS 0.009 0.002 HIS B 326 PHE 0.023 0.002 PHE A 372 TYR 0.021 0.002 TYR B 230 ARG 0.010 0.001 ARG B 269 *********************** 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 176 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 1.342 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6554 (mptt) cc_final: 0.5936 (mmmt) REVERT: A 272 LYS cc_start: 0.8653 (mmtt) cc_final: 0.7977 (mmtm) REVERT: A 335 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 387 ASP cc_start: 0.6229 (t0) cc_final: 0.5973 (t0) REVERT: A 798 CYS cc_start: 0.7917 (m) cc_final: 0.7412 (t) REVERT: A 801 TRP cc_start: 0.6789 (m100) cc_final: 0.6024 (m100) REVERT: B 48 ASP cc_start: 0.7816 (p0) cc_final: 0.7389 (p0) REVERT: B 118 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7397 (mm-40) REVERT: B 176 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7927 (tp40) REVERT: B 481 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: B 562 HIS cc_start: 0.8158 (t-90) cc_final: 0.7930 (t-90) REVERT: B 794 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7303 (tpt) outliers start: 46 outliers final: 29 residues processed: 168 average time/residue: 0.2068 time to fit residues: 52.4243 Evaluate side-chains 147 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 223 THR 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 481 GLN Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 777 THR Chi-restraints excluded: chain B residue 794 MET Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.9695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11445 Z= 0.232 Angle : 0.600 12.223 15625 Z= 0.296 Chirality : 0.043 0.182 1808 Planarity : 0.004 0.062 2051 Dihedral : 3.855 23.498 1662 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.92 % Allowed : 22.47 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1548 helix: 0.96 (0.20), residues: 696 sheet: -0.98 (0.46), residues: 142 loop : -2.08 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 368 HIS 0.004 0.001 HIS A 326 PHE 0.027 0.002 PHE A 612 TYR 0.017 0.001 TYR B 230 ARG 0.012 0.001 ARG B 269 *********************** 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 160 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6333 (mptt) cc_final: 0.5681 (mmmt) REVERT: A 272 LYS cc_start: 0.8624 (mmtt) cc_final: 0.8015 (mmtm) REVERT: A 335 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 387 ASP cc_start: 0.6215 (t0) cc_final: 0.5958 (t0) REVERT: A 801 TRP cc_start: 0.6921 (m100) cc_final: 0.6227 (m100) REVERT: B 48 ASP cc_start: 0.7771 (p0) cc_final: 0.7341 (p0) REVERT: B 118 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7211 (mm-40) REVERT: B 555 PHE cc_start: 0.7718 (m-80) cc_final: 0.7402 (m-80) REVERT: B 562 HIS cc_start: 0.8192 (t-90) cc_final: 0.7970 (t-90) REVERT: B 594 PRO cc_start: 0.9474 (Cg_exo) cc_final: 0.9247 (Cg_endo) outliers start: 41 outliers final: 28 residues processed: 152 average time/residue: 0.1976 time to fit residues: 45.6782 Evaluate side-chains 139 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 770 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER 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 455 VAL Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 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 777 THR Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 128 GLN B 88 GLN B 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.9901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11445 Z= 0.207 Angle : 0.590 9.931 15625 Z= 0.290 Chirality : 0.042 0.152 1808 Planarity : 0.004 0.037 2051 Dihedral : 3.708 22.231 1662 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.82 % Allowed : 22.37 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.21), residues: 1548 helix: 1.04 (0.20), residues: 708 sheet: -0.84 (0.46), residues: 142 loop : -2.05 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 368 HIS 0.003 0.001 HIS A 423 PHE 0.028 0.001 PHE B 684 TYR 0.018 0.001 TYR B 230 ARG 0.009 0.000 ARG B 269 *********************** 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 164 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6228 (mptt) cc_final: 0.5963 (mmmt) REVERT: A 272 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8067 (mmtm) REVERT: A 335 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 387 ASP cc_start: 0.6200 (t0) cc_final: 0.5946 (t0) REVERT: A 569 PRO cc_start: 0.6242 (Cg_endo) cc_final: 0.5985 (Cg_exo) REVERT: A 766 LEU cc_start: 0.5384 (pp) cc_final: 0.4719 (mp) REVERT: A 801 TRP cc_start: 0.6976 (m100) cc_final: 0.6140 (m100) REVERT: B 48 ASP cc_start: 0.7654 (p0) cc_final: 0.7354 (p0) REVERT: B 73 GLU cc_start: 0.7743 (pp20) cc_final: 0.7170 (pp20) REVERT: B 154 ILE cc_start: 0.9169 (OUTLIER) cc_final: 0.8956 (pt) REVERT: B 325 GLN cc_start: 0.7297 (tm-30) cc_final: 0.6833 (tp40) REVERT: B 481 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: B 794 MET cc_start: 0.7378 (tpt) cc_final: 0.7120 (tpt) outliers start: 40 outliers final: 25 residues processed: 155 average time/residue: 0.2060 time to fit residues: 47.8260 Evaluate side-chains 145 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER 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 455 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 95 optimal weight: 0.0270 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.0980 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11445 Z= 0.219 Angle : 0.599 13.102 15625 Z= 0.294 Chirality : 0.042 0.149 1808 Planarity : 0.004 0.037 2051 Dihedral : 3.697 21.844 1662 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.02 % Allowed : 22.28 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1548 helix: 1.09 (0.20), residues: 702 sheet: -0.70 (0.47), residues: 142 loop : -2.07 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 368 HIS 0.003 0.001 HIS A 423 PHE 0.029 0.001 PHE B 684 TYR 0.027 0.001 TYR B 681 ARG 0.006 0.000 ARG B 269 *********************** 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 163 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.5985 (mptt) cc_final: 0.5499 (mmmt) REVERT: A 272 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8082 (mmtm) REVERT: A 387 ASP cc_start: 0.6223 (t0) cc_final: 0.5964 (t0) REVERT: A 801 TRP cc_start: 0.7040 (m100) cc_final: 0.6142 (m100) REVERT: B 48 ASP cc_start: 0.7649 (p0) cc_final: 0.7379 (p0) REVERT: B 73 GLU cc_start: 0.7726 (pp20) cc_final: 0.7188 (pp20) REVERT: B 118 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7233 (mm-40) REVERT: B 154 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8937 (pt) REVERT: B 325 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6881 (tp40) REVERT: B 481 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8146 (tm-30) REVERT: B 594 PRO cc_start: 0.9515 (Cg_exo) cc_final: 0.9293 (Cg_endo) REVERT: B 607 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6172 (t80) REVERT: B 794 MET cc_start: 0.7415 (tpt) cc_final: 0.7178 (tpt) outliers start: 42 outliers final: 31 residues processed: 154 average time/residue: 0.1997 time to fit residues: 46.6926 Evaluate side-chains 153 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain A residue 770 CYS Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER 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 455 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 VAL Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 607 PHE Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 1.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 11445 Z= 0.440 Angle : 0.716 10.045 15625 Z= 0.358 Chirality : 0.046 0.263 1808 Planarity : 0.005 0.041 2051 Dihedral : 4.283 23.966 1662 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.02 % Allowed : 22.56 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.21), residues: 1548 helix: 0.99 (0.20), residues: 692 sheet: -1.01 (0.46), residues: 148 loop : -2.03 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 368 HIS 0.005 0.001 HIS A 423 PHE 0.028 0.002 PHE B 684 TYR 0.029 0.002 TYR B 681 ARG 0.007 0.001 ARG B 269 *********************** 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 162 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8026 (tpp) cc_final: 0.7693 (tpp) REVERT: A 562 HIS cc_start: 0.8016 (t-90) cc_final: 0.7810 (t-90) REVERT: A 801 TRP cc_start: 0.6879 (m100) cc_final: 0.6433 (m100) REVERT: B 48 ASP cc_start: 0.7883 (p0) cc_final: 0.7555 (p0) REVERT: B 73 GLU cc_start: 0.7787 (pp20) cc_final: 0.7343 (pp20) REVERT: B 118 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7768 (mm-40) REVERT: B 176 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8235 (tp40) REVERT: B 250 ILE cc_start: 0.9013 (tp) cc_final: 0.8767 (pt) REVERT: B 325 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7148 (tp40) REVERT: B 481 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: B 594 PRO cc_start: 0.9543 (Cg_exo) cc_final: 0.9338 (Cg_endo) REVERT: B 607 PHE cc_start: 0.7048 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 767 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7097 (ttt) REVERT: B 794 MET cc_start: 0.7568 (tpt) cc_final: 0.7281 (tpt) REVERT: B 844 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8079 (mmtm) outliers start: 42 outliers final: 31 residues processed: 157 average time/residue: 0.2011 time to fit residues: 47.9148 Evaluate side-chains 150 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 524 THR Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER 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 455 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 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 767 MET Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.3980 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 0.0060 chunk 143 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 1.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11445 Z= 0.234 Angle : 0.621 12.332 15625 Z= 0.305 Chirality : 0.043 0.165 1808 Planarity : 0.004 0.040 2051 Dihedral : 3.926 22.576 1662 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.25 % Allowed : 23.33 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1548 helix: 1.21 (0.20), residues: 676 sheet: -0.76 (0.47), residues: 146 loop : -2.00 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 368 HIS 0.002 0.001 HIS A 420 PHE 0.026 0.001 PHE B 684 TYR 0.026 0.001 TYR B 681 ARG 0.006 0.000 ARG B 269 ********************** 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 155 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.7929 (tpp) cc_final: 0.7663 (tpp) REVERT: A 801 TRP cc_start: 0.6932 (m100) cc_final: 0.6177 (m100) REVERT: B 48 ASP cc_start: 0.7785 (p0) cc_final: 0.7510 (p0) REVERT: B 73 GLU cc_start: 0.7671 (pp20) cc_final: 0.7233 (pp20) REVERT: B 250 ILE cc_start: 0.8992 (tp) cc_final: 0.8720 (pt) REVERT: B 325 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7093 (tp40) REVERT: B 481 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8282 (tm-30) REVERT: B 555 PHE cc_start: 0.7542 (m-80) cc_final: 0.7181 (m-80) REVERT: B 594 PRO cc_start: 0.9532 (Cg_exo) cc_final: 0.9330 (Cg_endo) REVERT: B 607 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6333 (t80) REVERT: B 767 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (ttt) REVERT: B 794 MET cc_start: 0.7516 (tpt) cc_final: 0.7249 (tpt) outliers start: 34 outliers final: 27 residues processed: 149 average time/residue: 0.1812 time to fit residues: 41.9414 Evaluate side-chains 147 residues out of total 1352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 119 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 455 VAL Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 503 GLN Chi-restraints excluded: chain B residue 522 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 767 MET Chi-restraints excluded: chain B residue 808 PHE Chi-restraints excluded: chain B residue 811 THR Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.3980 chunk 51 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 GLN B 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.137282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109702 restraints weight = 25951.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.107753 restraints weight = 35616.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.104896 restraints weight = 34191.798| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 1.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11445 Z= 0.187 Angle : 0.597 11.715 15625 Z= 0.291 Chirality : 0.042 0.186 1808 Planarity : 0.004 0.039 2051 Dihedral : 3.733 21.877 1662 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.06 % Allowed : 23.42 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.21), residues: 1548 helix: 1.25 (0.20), residues: 688 sheet: -0.61 (0.47), residues: 146 loop : -2.11 (0.21), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 368 HIS 0.002 0.000 HIS A 326 PHE 0.025 0.001 PHE B 684 TYR 0.026 0.001 TYR B 681 ARG 0.006 0.000 ARG B 269 =============================================================================== Job complete usr+sys time: 2308.37 seconds wall clock time: 42 minutes 42.09 seconds (2562.09 seconds total)