Starting phenix.real_space_refine on Thu Feb 5 15:44:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9b_71405/02_2026/9p9b_71405.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 132 5.16 5 Cl 4 4.86 5 C 11796 2.51 5 N 2916 2.21 5 O 3252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18100 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "B" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "C" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 389} Chain breaks: 1 Chain: "D" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3164 Classifications: {'peptide': 405} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 389} Chain breaks: 1 Chain: "H" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "F" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "G" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "E" Number of atoms: 1327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1327 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 169} Chain breaks: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.25 Number of scatterers: 18100 At special positions: 0 Unit cell: (131.13, 111.6, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 132 16.00 O 3252 8.00 N 2916 7.00 C 11796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.03 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " 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: 1.26 Conformation dependent library (CDL) restraints added in 779.8 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 22 sheets defined 58.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 483 through 491 Processing helix chain 'A' and resid 506 through 509 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 568 removed outlier: 3.555A pdb=" N VAL A 552 " --> pdb=" O TRP A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 617 through 643 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.527A pdb=" N GLY A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.721A pdb=" N TYR A 733 " --> pdb=" O THR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 840 removed outlier: 3.703A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 839 " --> pdb=" O GLU A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 437 Processing helix chain 'B' and resid 438 through 441 Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 483 through 491 Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 535 through 541 removed outlier: 4.676A pdb=" N PHE B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 568 removed outlier: 3.778A pdb=" N ILE B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 607 Processing helix chain 'B' and resid 617 through 646 removed outlier: 3.619A pdb=" N ALA B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN B 641 " --> pdb=" O SER B 637 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA B 644 " --> pdb=" O ALA B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 664 Processing helix chain 'B' and resid 675 through 684 removed outlier: 3.797A pdb=" N GLU B 679 " --> pdb=" O GLY B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 699 Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 735 removed outlier: 3.850A pdb=" N TYR B 733 " --> pdb=" O THR B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 790 through 793 removed outlier: 3.562A pdb=" N GLY B 793 " --> pdb=" O TYR B 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 790 through 793' Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 839 removed outlier: 3.558A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY B 826 " --> pdb=" O VAL B 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 483 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 537 through 541 Processing helix chain 'C' and resid 544 through 566 removed outlier: 3.533A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 607 Processing helix chain 'C' and resid 617 through 643 Processing helix chain 'C' and resid 658 through 663 Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 686 through 697 Processing helix chain 'C' and resid 707 through 718 Processing helix chain 'C' and resid 728 through 736 Processing helix chain 'C' and resid 764 through 778 removed outlier: 3.887A pdb=" N VAL C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 773 " --> pdb=" O ASN C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 803 through 807 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 839 removed outlier: 3.596A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET C 829 " --> pdb=" O LEU C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 437 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 445 through 459 removed outlier: 3.793A pdb=" N LYS D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 535 through 541 removed outlier: 4.630A pdb=" N PHE D 539 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 568 removed outlier: 3.603A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 607 Processing helix chain 'D' and resid 617 through 640 removed outlier: 3.623A pdb=" N VAL D 623 " --> pdb=" O SER D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 663 Processing helix chain 'D' and resid 675 through 684 removed outlier: 3.599A pdb=" N ARG D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 699 Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 727 through 735 Processing helix chain 'D' and resid 764 through 778 removed outlier: 3.541A pdb=" N LEU D 773 " --> pdb=" O ASN D 769 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 778 " --> pdb=" O LYS D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 789 Processing helix chain 'D' and resid 796 through 803 removed outlier: 5.760A pdb=" N GLY D 801 " --> pdb=" O LYS D 798 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 803 " --> pdb=" O SER D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 813 Processing helix chain 'D' and resid 814 through 840 removed outlier: 3.533A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY D 826 " --> pdb=" O VAL D 822 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR D 838 " --> pdb=" O ILE D 834 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 29 removed outlier: 4.039A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.574A pdb=" N ARG H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 125 removed outlier: 3.766A pdb=" N LEU H 115 " --> pdb=" O SER H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.600A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 210 removed outlier: 3.619A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE H 201 " --> pdb=" O ALA H 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 30 removed outlier: 3.996A pdb=" N LEU F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE F 18 " --> pdb=" O THR F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.608A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.681A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN F 160 " --> pdb=" O TYR F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'G' and resid 8 through 30 removed outlier: 3.630A pdb=" N PHE G 18 " --> pdb=" O THR G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 105 through 125 Processing helix chain 'G' and resid 132 through 160 Processing helix chain 'G' and resid 177 through 210 removed outlier: 3.745A pdb=" N GLY G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 105 through 123 removed outlier: 3.842A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 159 Processing helix chain 'E' and resid 177 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 417 through 421 removed outlier: 6.470A pdb=" N VAL A 417 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ALA A 465 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 419 " --> pdb=" O ALA A 465 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA3, first strand: chain 'A' and resid 511 through 513 Processing sheet with id=AA4, first strand: chain 'A' and resid 518 through 520 removed outlier: 4.335A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.531A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 462 through 466 removed outlier: 3.527A pdb=" N THR B 421 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 496 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA8, first strand: chain 'B' and resid 511 through 513 Processing sheet with id=AA9, first strand: chain 'B' and resid 518 through 520 removed outlier: 3.854A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 704 through 705 removed outlier: 8.278A pdb=" N THR B 705 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR B 671 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 10.989A pdb=" N LEU B 672 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 462 through 466 removed outlier: 3.665A pdb=" N ILE C 496 " --> pdb=" O VAL C 418 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 511 through 520 removed outlier: 4.951A pdb=" N VAL C 756 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 754 " --> pdb=" O PRO C 516 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET C 518 " --> pdb=" O LYS C 752 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS C 752 " --> pdb=" O MET C 518 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 704 through 705 removed outlier: 9.280A pdb=" N THR C 705 " --> pdb=" O TYR C 669 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR C 671 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 10.366A pdb=" N LEU C 672 " --> pdb=" O GLU C 727 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 462 through 466 removed outlier: 6.529A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA D 465 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 419 " --> pdb=" O ALA D 465 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB7, first strand: chain 'D' and resid 511 through 520 removed outlier: 5.485A pdb=" N VAL D 756 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TYR D 754 " --> pdb=" O PRO D 516 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET D 518 " --> pdb=" O LYS D 752 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS D 752 " --> pdb=" O MET D 518 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 524 through 527 removed outlier: 4.012A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.285A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'H' and resid 77 through 79 removed outlier: 4.030A pdb=" N MET H 58 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC3, first strand: chain 'G' and resid 77 through 79 Processing sheet with id=AC4, first strand: chain 'E' and resid 78 through 79 1040 hydrogen bonds defined for protein. 2979 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: 3.22 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.19: 16 1.19 - 1.36: 5524 1.36 - 1.52: 7409 1.52 - 1.68: 5347 1.68 - 1.85: 220 Bond restraints: 18516 Sorted by residual: bond pdb=" C4 CYZ C 902 " pdb=" C5 CYZ C 902 " ideal model delta sigma weight residual 1.512 1.029 0.483 2.00e-02 2.50e+03 5.83e+02 bond pdb=" C4 CYZ A 902 " pdb=" C5 CYZ A 902 " ideal model delta sigma weight residual 1.512 1.030 0.482 2.00e-02 2.50e+03 5.80e+02 bond pdb=" C4 CYZ B 902 " pdb=" C5 CYZ B 902 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.79e+02 bond pdb=" C4 CYZ D 902 " pdb=" C5 CYZ D 902 " ideal model delta sigma weight residual 1.512 1.032 0.480 2.00e-02 2.50e+03 5.77e+02 bond pdb=" C5 CYZ C 902 " pdb=" C6 CYZ C 902 " ideal model delta sigma weight residual 1.553 1.073 0.480 2.00e-02 2.50e+03 5.76e+02 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 24908 4.33 - 8.66: 90 8.66 - 12.99: 6 12.99 - 17.32: 10 17.32 - 21.65: 6 Bond angle restraints: 25020 Sorted by residual: angle pdb=" C1 CYZ A 902 " pdb=" C2 CYZ A 902 " pdb=" C3 CYZ A 902 " ideal model delta sigma weight residual 106.92 128.57 -21.65 3.00e+00 1.11e-01 5.21e+01 angle pdb=" C1 CYZ C 902 " pdb=" C2 CYZ C 902 " pdb=" C3 CYZ C 902 " ideal model delta sigma weight residual 106.92 128.56 -21.64 3.00e+00 1.11e-01 5.21e+01 angle pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C3 CYZ B 902 " ideal model delta sigma weight residual 106.92 128.21 -21.29 3.00e+00 1.11e-01 5.04e+01 angle pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C3 CYZ D 902 " ideal model delta sigma weight residual 106.92 128.14 -21.22 3.00e+00 1.11e-01 5.00e+01 angle pdb=" O3 CYZ C 902 " pdb=" S2 CYZ C 902 " pdb=" O4 CYZ C 902 " ideal model delta sigma weight residual 118.35 100.76 17.59 3.00e+00 1.11e-01 3.44e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.94: 10419 22.94 - 45.89: 413 45.89 - 68.83: 38 68.83 - 91.77: 31 91.77 - 114.72: 9 Dihedral angle restraints: 10910 sinusoidal: 4314 harmonic: 6596 Sorted by residual: dihedral pdb=" CA PHE C 563 " pdb=" C PHE C 563 " pdb=" N LEU C 564 " pdb=" CA LEU C 564 " ideal model delta harmonic sigma weight residual 180.00 151.21 28.79 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA PHE B 836 " pdb=" C PHE B 836 " pdb=" N CYS B 837 " pdb=" CA CYS B 837 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASP F 81 " pdb=" C ASP F 81 " pdb=" N HIS F 82 " pdb=" CA HIS F 82 " ideal model delta harmonic sigma weight residual -180.00 -152.32 -27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 10907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.427: 2784 0.427 - 0.854: 8 0.854 - 1.281: 0 1.281 - 1.709: 0 1.709 - 2.136: 8 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C5 CYZ A 902 " pdb=" C4 CYZ A 902 " pdb=" C6 CYZ A 902 " pdb=" C7 CYZ A 902 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ D 902 " pdb=" C4 CYZ D 902 " pdb=" C6 CYZ D 902 " pdb=" C7 CYZ D 902 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.14 2.00e-01 2.50e+01 1.14e+02 chirality pdb=" C5 CYZ C 902 " pdb=" C4 CYZ C 902 " pdb=" C6 CYZ C 902 " pdb=" C7 CYZ C 902 " both_signs ideal model delta sigma weight residual False 3.31 1.17 2.13 2.00e-01 2.50e+01 1.14e+02 ... (remaining 2797 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 833 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C LEU B 833 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU B 833 " 0.022 2.00e-02 2.50e+03 pdb=" N ILE B 834 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 559 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.18e+00 pdb=" C SER B 559 " -0.052 2.00e-02 2.50e+03 pdb=" O SER B 559 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL B 560 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 822 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C VAL C 822 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL C 822 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY C 823 " 0.018 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 967 2.73 - 3.27: 19377 3.27 - 3.81: 29417 3.81 - 4.36: 36448 4.36 - 4.90: 62053 Nonbonded interactions: 148262 Sorted by model distance: nonbonded pdb=" OG SER A 519 " pdb=" O2 CYZ A 902 " model vdw 2.186 3.040 nonbonded pdb=" OE2 GLU D 424 " pdb=" OH TYR D 472 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR E 59 " pdb=" O CYS E 67 " model vdw 2.260 3.040 nonbonded pdb=" OD2 ASP D 750 " pdb=" NZ LYS D 752 " model vdw 2.290 3.120 nonbonded pdb=" NH1 ARG D 567 " pdb=" O GLY D 594 " model vdw 2.292 3.120 ... (remaining 148257 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.016 0.483 18526 Z= 0.810 Angle : 0.884 21.651 25040 Z= 0.447 Chirality : 0.123 2.136 2800 Planarity : 0.008 0.099 3056 Dihedral : 13.743 114.715 6672 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.26 % Favored : 95.43 % Rotamer: Outliers : 0.05 % Allowed : 1.77 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -1.90 (0.16), residues: 2256 helix: -1.09 (0.12), residues: 1273 sheet: -1.25 (0.42), residues: 156 loop : -1.26 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.003 ARG H 65 TYR 0.028 0.004 TYR A 430 PHE 0.034 0.002 PHE A 568 TRP 0.029 0.002 TRP F 178 HIS 0.009 0.001 HIS A 434 Details of bonding type rmsd covalent geometry : bond 0.01629 (18516) covalent geometry : angle 0.88439 (25020) SS BOND : bond 0.00288 ( 10) SS BOND : angle 0.83452 ( 20) hydrogen bonds : bond 0.12459 ( 1040) hydrogen bonds : angle 6.35817 ( 2979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 572 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8209 (tttt) cc_final: 0.7997 (mtpp) REVERT: A 446 TYR cc_start: 0.8271 (t80) cc_final: 0.7946 (t80) REVERT: A 482 TRP cc_start: 0.7735 (m100) cc_final: 0.7377 (m100) REVERT: A 567 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7394 (mtm180) REVERT: A 672 LEU cc_start: 0.7863 (tt) cc_final: 0.7457 (tt) REVERT: A 678 LYS cc_start: 0.9075 (tttt) cc_final: 0.8826 (ttmt) REVERT: A 710 GLU cc_start: 0.8115 (tt0) cc_final: 0.7830 (tt0) REVERT: A 790 TYR cc_start: 0.7780 (m-80) cc_final: 0.7531 (t80) REVERT: A 833 LEU cc_start: 0.7299 (tt) cc_final: 0.6592 (mp) REVERT: B 430 TYR cc_start: 0.8304 (m-80) cc_final: 0.7269 (m-10) REVERT: B 440 ASN cc_start: 0.8388 (m-40) cc_final: 0.8102 (m-40) REVERT: B 508 GLU cc_start: 0.8277 (tp30) cc_final: 0.7998 (tp30) REVERT: B 667 ILE cc_start: 0.7577 (mt) cc_final: 0.7073 (mm) REVERT: B 693 TRP cc_start: 0.8350 (t-100) cc_final: 0.8047 (t-100) REVERT: B 736 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8080 (mm-40) REVERT: B 738 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8368 (mmmt) REVERT: B 743 MET cc_start: 0.7956 (ptm) cc_final: 0.7636 (ptp) REVERT: B 782 ASP cc_start: 0.8776 (m-30) cc_final: 0.8086 (t0) REVERT: B 786 ASN cc_start: 0.8577 (m-40) cc_final: 0.7965 (m110) REVERT: C 513 PHE cc_start: 0.7591 (m-80) cc_final: 0.7390 (m-10) REVERT: C 525 MET cc_start: 0.8171 (ttm) cc_final: 0.7718 (ttp) REVERT: C 541 ASP cc_start: 0.8317 (m-30) cc_final: 0.7838 (m-30) REVERT: C 567 ARG cc_start: 0.7496 (tpp-160) cc_final: 0.7169 (tpp80) REVERT: C 735 GLU cc_start: 0.8422 (tt0) cc_final: 0.7861 (pt0) REVERT: C 743 MET cc_start: 0.6668 (ptt) cc_final: 0.6098 (tpp) REVERT: C 744 LYS cc_start: 0.8188 (tttt) cc_final: 0.7762 (tttp) REVERT: C 783 LYS cc_start: 0.8510 (tttt) cc_final: 0.8062 (tptt) REVERT: C 788 TRP cc_start: 0.8455 (m100) cc_final: 0.8019 (m100) REVERT: D 441 ASP cc_start: 0.8854 (m-30) cc_final: 0.8285 (p0) REVERT: D 453 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 476 ASP cc_start: 0.6508 (t0) cc_final: 0.5064 (t70) REVERT: D 478 ASP cc_start: 0.7931 (m-30) cc_final: 0.7348 (p0) REVERT: D 511 ILE cc_start: 0.8459 (pt) cc_final: 0.8103 (mt) REVERT: D 533 LYS cc_start: 0.7599 (mptt) cc_final: 0.7327 (mttm) REVERT: D 541 ASP cc_start: 0.8294 (m-30) cc_final: 0.7809 (t70) REVERT: D 660 ASP cc_start: 0.8054 (m-30) cc_final: 0.7768 (m-30) REVERT: D 676 SER cc_start: 0.8857 (t) cc_final: 0.8558 (m) REVERT: D 692 MET cc_start: 0.8887 (mtp) cc_final: 0.8337 (mmm) REVERT: D 710 GLU cc_start: 0.7746 (tt0) cc_final: 0.7487 (tm-30) REVERT: D 735 GLU cc_start: 0.7512 (tt0) cc_final: 0.7221 (tt0) REVERT: D 741 ASP cc_start: 0.8165 (p0) cc_final: 0.7873 (p0) REVERT: D 786 ASN cc_start: 0.8596 (m-40) cc_final: 0.8188 (m110) REVERT: H 18 PHE cc_start: 0.8366 (t80) cc_final: 0.8113 (t80) REVERT: F 24 MET cc_start: 0.7755 (tpt) cc_final: 0.7473 (tpp) REVERT: G 32 TYR cc_start: 0.8526 (m-80) cc_final: 0.8181 (m-10) REVERT: G 99 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7510 (tpp80) REVERT: G 120 LEU cc_start: 0.7969 (tt) cc_final: 0.7687 (mp) REVERT: G 175 SER cc_start: 0.8311 (p) cc_final: 0.8075 (m) REVERT: E 37 ARG cc_start: 0.7691 (mmt180) cc_final: 0.7362 (mmp80) REVERT: E 203 ASP cc_start: 0.8061 (t0) cc_final: 0.7732 (t70) outliers start: 1 outliers final: 0 residues processed: 573 average time/residue: 0.1687 time to fit residues: 136.5816 Evaluate side-chains 355 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0970 chunk 200 optimal weight: 9.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN A 608 GLN A 736 GLN A 769 ASN B 769 ASN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN F 133 ASN G 199 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.195003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.120727 restraints weight = 22858.805| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.57 r_work: 0.3382 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18526 Z= 0.146 Angle : 0.635 8.970 25040 Z= 0.335 Chirality : 0.043 0.219 2800 Planarity : 0.004 0.045 3056 Dihedral : 9.181 96.313 2596 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.35 % Favored : 97.47 % Rotamer: Outliers : 2.13 % Allowed : 11.28 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 0.11 (0.18), residues: 2256 helix: 0.99 (0.15), residues: 1281 sheet: -1.21 (0.40), residues: 154 loop : -1.07 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 737 TYR 0.022 0.001 TYR B 430 PHE 0.025 0.002 PHE B 836 TRP 0.021 0.001 TRP F 178 HIS 0.007 0.001 HIS H 132 Details of bonding type rmsd covalent geometry : bond 0.00329 (18516) covalent geometry : angle 0.62937 (25020) SS BOND : bond 0.01045 ( 10) SS BOND : angle 2.93411 ( 20) hydrogen bonds : bond 0.04162 ( 1040) hydrogen bonds : angle 4.43723 ( 2979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 409 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5843 (OUTLIER) cc_final: 0.5557 (p0) REVERT: A 442 LYS cc_start: 0.8072 (tttt) cc_final: 0.7846 (mtpp) REVERT: A 446 TYR cc_start: 0.8136 (t80) cc_final: 0.7778 (t80) REVERT: A 567 ARG cc_start: 0.8614 (mtp180) cc_final: 0.7798 (mtt90) REVERT: A 607 MET cc_start: 0.8452 (mmt) cc_final: 0.7474 (mmt) REVERT: A 672 LEU cc_start: 0.7558 (tt) cc_final: 0.7052 (tt) REVERT: A 678 LYS cc_start: 0.8927 (tttt) cc_final: 0.8538 (ttmt) REVERT: A 710 GLU cc_start: 0.8126 (tt0) cc_final: 0.7773 (tt0) REVERT: A 714 ARG cc_start: 0.8330 (tpt-90) cc_final: 0.8100 (ttt180) REVERT: A 790 TYR cc_start: 0.7980 (m-80) cc_final: 0.7763 (t80) REVERT: A 833 LEU cc_start: 0.7490 (tt) cc_final: 0.6929 (mm) REVERT: B 505 LEU cc_start: 0.8901 (pp) cc_final: 0.8649 (pp) REVERT: B 508 GLU cc_start: 0.8339 (tp30) cc_final: 0.7801 (tp30) REVERT: B 511 ILE cc_start: 0.8359 (mm) cc_final: 0.7663 (tt) REVERT: B 567 ARG cc_start: 0.6613 (mtt90) cc_final: 0.4140 (mtt180) REVERT: B 616 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8527 (ttm110) REVERT: B 667 ILE cc_start: 0.7438 (mt) cc_final: 0.7000 (mm) REVERT: B 738 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8301 (mmmt) REVERT: B 782 ASP cc_start: 0.8837 (m-30) cc_final: 0.8227 (t70) REVERT: B 786 ASN cc_start: 0.8573 (m-40) cc_final: 0.8055 (m-40) REVERT: C 482 TRP cc_start: 0.8232 (m-90) cc_final: 0.7185 (m-90) REVERT: C 525 MET cc_start: 0.7921 (ttm) cc_final: 0.7437 (ttp) REVERT: C 541 ASP cc_start: 0.8500 (m-30) cc_final: 0.7956 (m-30) REVERT: C 685 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8586 (mmmt) REVERT: C 704 PHE cc_start: 0.8454 (m-10) cc_final: 0.8254 (m-10) REVERT: C 717 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8220 (ptpt) REVERT: C 727 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7078 (mp0) REVERT: C 735 GLU cc_start: 0.8514 (tt0) cc_final: 0.7948 (pt0) REVERT: C 743 MET cc_start: 0.6346 (ptt) cc_final: 0.5845 (tpp) REVERT: C 744 LYS cc_start: 0.7974 (tttt) cc_final: 0.7615 (tttp) REVERT: C 783 LYS cc_start: 0.8618 (tttt) cc_final: 0.8165 (tppt) REVERT: C 788 TRP cc_start: 0.8249 (m100) cc_final: 0.7943 (m100) REVERT: D 425 SER cc_start: 0.8985 (m) cc_final: 0.8725 (t) REVERT: D 453 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6777 (mm-30) REVERT: D 478 ASP cc_start: 0.7980 (m-30) cc_final: 0.7479 (p0) REVERT: D 512 ASP cc_start: 0.7349 (m-30) cc_final: 0.6797 (p0) REVERT: D 533 LYS cc_start: 0.7705 (mptt) cc_final: 0.7340 (mttm) REVERT: D 541 ASP cc_start: 0.8413 (m-30) cc_final: 0.7996 (t0) REVERT: D 607 MET cc_start: 0.8732 (mmt) cc_final: 0.8424 (mmt) REVERT: D 676 SER cc_start: 0.8751 (t) cc_final: 0.8283 (m) REVERT: D 692 MET cc_start: 0.8987 (mtp) cc_final: 0.8330 (mmm) REVERT: D 732 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8013 (tt0) REVERT: D 741 ASP cc_start: 0.8246 (p0) cc_final: 0.7911 (p0) REVERT: D 786 ASN cc_start: 0.8469 (m-40) cc_final: 0.8264 (m110) REVERT: G 32 TYR cc_start: 0.8487 (m-80) cc_final: 0.8218 (m-10) REVERT: G 115 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7875 (mt) REVERT: G 120 LEU cc_start: 0.7887 (tt) cc_final: 0.7604 (mp) REVERT: G 131 ARG cc_start: 0.7423 (ttt180) cc_final: 0.6920 (mmm160) REVERT: E 79 GLN cc_start: 0.7566 (mp10) cc_final: 0.7358 (mp10) REVERT: E 203 ASP cc_start: 0.8042 (t0) cc_final: 0.7740 (t70) REVERT: E 205 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6299 (t-90) outliers start: 41 outliers final: 20 residues processed: 434 average time/residue: 0.1511 time to fit residues: 97.2356 Evaluate side-chains 365 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 745 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 111 SER Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 205 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 148 optimal weight: 0.1980 chunk 204 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 HIS A 736 GLN A 748 ASN B 769 ASN C 457 HIS ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS E 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.192311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.121516 restraints weight = 22937.783| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 3.10 r_work: 0.3305 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18526 Z= 0.161 Angle : 0.611 15.996 25040 Z= 0.319 Chirality : 0.043 0.244 2800 Planarity : 0.004 0.046 3056 Dihedral : 8.611 91.800 2596 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 2.75 % Allowed : 13.05 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 0.56 (0.18), residues: 2256 helix: 1.46 (0.15), residues: 1284 sheet: -1.25 (0.41), residues: 143 loop : -1.04 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 37 TYR 0.021 0.001 TYR C 472 PHE 0.031 0.001 PHE B 836 TRP 0.013 0.001 TRP F 178 HIS 0.018 0.002 HIS G 199 Details of bonding type rmsd covalent geometry : bond 0.00388 (18516) covalent geometry : angle 0.60603 (25020) SS BOND : bond 0.00740 ( 10) SS BOND : angle 2.90498 ( 20) hydrogen bonds : bond 0.04006 ( 1040) hydrogen bonds : angle 4.20084 ( 2979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 363 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7819 (mmm) cc_final: 0.7414 (mmm) REVERT: A 433 ASN cc_start: 0.5883 (OUTLIER) cc_final: 0.5568 (p0) REVERT: A 442 LYS cc_start: 0.8126 (tttt) cc_final: 0.7864 (mtpp) REVERT: A 443 TYR cc_start: 0.9090 (m-80) cc_final: 0.8126 (m-10) REVERT: A 446 TYR cc_start: 0.8064 (t80) cc_final: 0.7695 (t80) REVERT: A 518 MET cc_start: 0.6586 (ttm) cc_final: 0.6361 (ttm) REVERT: A 567 ARG cc_start: 0.8679 (mtp180) cc_final: 0.8052 (mtt90) REVERT: A 672 LEU cc_start: 0.7526 (tt) cc_final: 0.6900 (tt) REVERT: A 678 LYS cc_start: 0.8852 (tttt) cc_final: 0.8601 (ttmt) REVERT: A 690 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7803 (mt-10) REVERT: A 710 GLU cc_start: 0.8086 (tt0) cc_final: 0.7736 (tt0) REVERT: A 833 LEU cc_start: 0.7524 (tt) cc_final: 0.7024 (mm) REVERT: B 441 ASP cc_start: 0.8160 (m-30) cc_final: 0.7725 (t70) REVERT: B 485 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.7869 (mmp) REVERT: B 508 GLU cc_start: 0.8366 (tp30) cc_final: 0.7770 (tp30) REVERT: B 567 ARG cc_start: 0.6486 (mtt90) cc_final: 0.3993 (mtt180) REVERT: B 616 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8411 (ttm110) REVERT: B 738 LYS cc_start: 0.8875 (mtpt) cc_final: 0.8328 (mmmt) REVERT: B 782 ASP cc_start: 0.8769 (m-30) cc_final: 0.8192 (t70) REVERT: B 786 ASN cc_start: 0.8500 (m-40) cc_final: 0.7975 (m-40) REVERT: B 819 TYR cc_start: 0.8906 (m-10) cc_final: 0.8462 (m-80) REVERT: C 472 TYR cc_start: 0.8532 (m-80) cc_final: 0.8244 (m-80) REVERT: C 475 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7751 (ttp80) REVERT: C 482 TRP cc_start: 0.8168 (m-90) cc_final: 0.7181 (m-90) REVERT: C 525 MET cc_start: 0.7997 (ttm) cc_final: 0.7336 (ttp) REVERT: C 541 ASP cc_start: 0.8419 (m-30) cc_final: 0.7893 (m-30) REVERT: C 685 LYS cc_start: 0.8912 (mmtm) cc_final: 0.8568 (mmmt) REVERT: C 727 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: C 783 LYS cc_start: 0.8621 (tttt) cc_final: 0.8250 (tptt) REVERT: C 788 TRP cc_start: 0.8355 (m100) cc_final: 0.8143 (m100) REVERT: D 425 SER cc_start: 0.9007 (m) cc_final: 0.8755 (t) REVERT: D 453 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6712 (mm-30) REVERT: D 533 LYS cc_start: 0.7792 (mptt) cc_final: 0.7289 (mttm) REVERT: D 541 ASP cc_start: 0.8227 (m-30) cc_final: 0.7873 (t0) REVERT: D 676 SER cc_start: 0.8842 (t) cc_final: 0.8312 (m) REVERT: D 692 MET cc_start: 0.8994 (mtp) cc_final: 0.8373 (mmp) REVERT: D 732 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7919 (tt0) REVERT: D 786 ASN cc_start: 0.8602 (m-40) cc_final: 0.8311 (m110) REVERT: H 79 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: G 120 LEU cc_start: 0.7922 (tt) cc_final: 0.7679 (mp) REVERT: G 131 ARG cc_start: 0.7543 (ttt180) cc_final: 0.7046 (mmm160) REVERT: E 79 GLN cc_start: 0.7687 (mp10) cc_final: 0.7478 (mp10) REVERT: E 149 ASN cc_start: 0.8665 (t0) cc_final: 0.8227 (t0) REVERT: E 203 ASP cc_start: 0.8100 (t0) cc_final: 0.7712 (t70) outliers start: 53 outliers final: 31 residues processed: 393 average time/residue: 0.1438 time to fit residues: 84.8973 Evaluate side-chains 360 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 616 ARG Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 CYS Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 198 VAL Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 205 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 211 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS E 205 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.190463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119535 restraints weight = 22851.269| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.02 r_work: 0.3283 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18526 Z= 0.178 Angle : 0.609 13.390 25040 Z= 0.316 Chirality : 0.043 0.185 2800 Planarity : 0.004 0.046 3056 Dihedral : 8.132 87.534 2596 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.79 % Favored : 97.07 % Rotamer: Outliers : 2.86 % Allowed : 14.45 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2256 helix: 1.57 (0.15), residues: 1287 sheet: -1.23 (0.40), residues: 145 loop : -1.12 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 737 TYR 0.016 0.001 TYR A 427 PHE 0.026 0.001 PHE C 563 TRP 0.022 0.002 TRP G 178 HIS 0.017 0.002 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00433 (18516) covalent geometry : angle 0.60366 (25020) SS BOND : bond 0.00690 ( 10) SS BOND : angle 2.86194 ( 20) hydrogen bonds : bond 0.04056 ( 1040) hydrogen bonds : angle 4.13544 ( 2979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5770 (OUTLIER) cc_final: 0.5447 (p0) REVERT: A 442 LYS cc_start: 0.8108 (tttt) cc_final: 0.7801 (mttm) REVERT: A 485 MET cc_start: 0.9331 (mtp) cc_final: 0.8544 (mmt) REVERT: A 518 MET cc_start: 0.6830 (ttm) cc_final: 0.6557 (ttm) REVERT: A 567 ARG cc_start: 0.8858 (mtp180) cc_final: 0.8187 (mtt90) REVERT: A 678 LYS cc_start: 0.8923 (tttt) cc_final: 0.8709 (ttmt) REVERT: A 690 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7817 (mp0) REVERT: A 692 MET cc_start: 0.8938 (mpp) cc_final: 0.8735 (mpp) REVERT: A 710 GLU cc_start: 0.8220 (tt0) cc_final: 0.7885 (tt0) REVERT: A 833 LEU cc_start: 0.7653 (tt) cc_final: 0.7177 (mm) REVERT: B 441 ASP cc_start: 0.8170 (m-30) cc_final: 0.7725 (t70) REVERT: B 485 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.7785 (mmp) REVERT: B 508 GLU cc_start: 0.8443 (tp30) cc_final: 0.7784 (tp30) REVERT: B 567 ARG cc_start: 0.6623 (mtt90) cc_final: 0.3921 (mtt180) REVERT: B 667 ILE cc_start: 0.7502 (mt) cc_final: 0.7162 (mm) REVERT: B 678 LYS cc_start: 0.8153 (tttt) cc_final: 0.7697 (tttm) REVERT: B 738 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8276 (mmmt) REVERT: B 782 ASP cc_start: 0.8825 (m-30) cc_final: 0.8253 (t70) REVERT: B 786 ASN cc_start: 0.8507 (m-40) cc_final: 0.7947 (m-40) REVERT: B 819 TYR cc_start: 0.8939 (m-10) cc_final: 0.8530 (m-80) REVERT: C 453 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8648 (mm-30) REVERT: C 472 TYR cc_start: 0.8542 (m-80) cc_final: 0.8231 (m-80) REVERT: C 475 ARG cc_start: 0.8436 (ttp80) cc_final: 0.7838 (ttp80) REVERT: C 482 TRP cc_start: 0.8317 (m-90) cc_final: 0.7644 (m-90) REVERT: C 525 MET cc_start: 0.7915 (ttm) cc_final: 0.7562 (ttp) REVERT: C 541 ASP cc_start: 0.8498 (m-30) cc_final: 0.8214 (m-30) REVERT: C 645 PHE cc_start: 0.8523 (t80) cc_final: 0.8020 (t80) REVERT: C 727 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: C 783 LYS cc_start: 0.8660 (tttt) cc_final: 0.8246 (tptt) REVERT: C 807 SER cc_start: 0.8011 (p) cc_final: 0.7743 (t) REVERT: D 423 MET cc_start: 0.7427 (tpp) cc_final: 0.7103 (tpt) REVERT: D 453 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6819 (mm-30) REVERT: D 485 MET cc_start: 0.6920 (mmm) cc_final: 0.6357 (mmt) REVERT: D 530 GLN cc_start: 0.8420 (tp40) cc_final: 0.8092 (mm-40) REVERT: D 533 LYS cc_start: 0.7845 (mptt) cc_final: 0.7209 (mttm) REVERT: D 541 ASP cc_start: 0.8396 (m-30) cc_final: 0.7998 (t0) REVERT: D 676 SER cc_start: 0.8867 (t) cc_final: 0.8306 (m) REVERT: D 692 MET cc_start: 0.9006 (mtp) cc_final: 0.8496 (mmm) REVERT: D 704 PHE cc_start: 0.7639 (m-80) cc_final: 0.7414 (m-80) REVERT: D 732 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8017 (tt0) REVERT: D 786 ASN cc_start: 0.8647 (m-40) cc_final: 0.8339 (m110) REVERT: H 10 MET cc_start: 0.8630 (tpp) cc_final: 0.8362 (mmm) REVERT: H 79 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8083 (mp10) REVERT: G 120 LEU cc_start: 0.7959 (tt) cc_final: 0.7692 (mp) REVERT: G 131 ARG cc_start: 0.7619 (ttt180) cc_final: 0.6979 (mmm160) REVERT: E 149 ASN cc_start: 0.8763 (t0) cc_final: 0.8330 (t0) REVERT: E 203 ASP cc_start: 0.8181 (t0) cc_final: 0.7764 (t70) outliers start: 55 outliers final: 29 residues processed: 381 average time/residue: 0.1483 time to fit residues: 84.5649 Evaluate side-chains 365 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 743 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 740 CYS Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 205 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.4980 chunk 165 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 199 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 457 HIS C 736 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS E 205 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.192609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118280 restraints weight = 22589.556| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.49 r_work: 0.3340 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18526 Z= 0.126 Angle : 0.571 11.323 25040 Z= 0.294 Chirality : 0.041 0.182 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.568 80.335 2596 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.62 % Favored : 97.25 % Rotamer: Outliers : 2.23 % Allowed : 16.11 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 0.90 (0.18), residues: 2256 helix: 1.86 (0.15), residues: 1289 sheet: -1.27 (0.39), residues: 146 loop : -1.12 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 37 TYR 0.018 0.001 TYR D 733 PHE 0.016 0.001 PHE B 836 TRP 0.024 0.001 TRP C 788 HIS 0.019 0.002 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00293 (18516) covalent geometry : angle 0.56794 (25020) SS BOND : bond 0.00543 ( 10) SS BOND : angle 2.14102 ( 20) hydrogen bonds : bond 0.03632 ( 1040) hydrogen bonds : angle 3.95399 ( 2979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 355 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5848 (OUTLIER) cc_final: 0.5509 (p0) REVERT: A 442 LYS cc_start: 0.8156 (tttt) cc_final: 0.7781 (mttm) REVERT: A 485 MET cc_start: 0.9321 (mtp) cc_final: 0.8561 (mmt) REVERT: A 518 MET cc_start: 0.6723 (ttm) cc_final: 0.6505 (ttm) REVERT: A 567 ARG cc_start: 0.8784 (mtp180) cc_final: 0.8097 (mtt90) REVERT: A 666 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7549 (tm-30) REVERT: A 690 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7823 (mp0) REVERT: A 710 GLU cc_start: 0.8164 (tt0) cc_final: 0.7824 (tt0) REVERT: A 833 LEU cc_start: 0.7584 (tt) cc_final: 0.7190 (mm) REVERT: B 441 ASP cc_start: 0.8184 (m-30) cc_final: 0.7741 (t70) REVERT: B 485 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.7812 (mmt) REVERT: B 491 TYR cc_start: 0.8161 (m-80) cc_final: 0.7838 (m-80) REVERT: B 508 GLU cc_start: 0.8441 (tp30) cc_final: 0.7729 (tp30) REVERT: B 567 ARG cc_start: 0.6558 (mtt90) cc_final: 0.3941 (mtt180) REVERT: B 669 TYR cc_start: 0.7750 (p90) cc_final: 0.7538 (p90) REVERT: B 678 LYS cc_start: 0.7991 (tttt) cc_final: 0.7654 (tttt) REVERT: B 696 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: B 782 ASP cc_start: 0.8820 (m-30) cc_final: 0.8213 (t70) REVERT: B 786 ASN cc_start: 0.8481 (m-40) cc_final: 0.7913 (m-40) REVERT: B 819 TYR cc_start: 0.8901 (m-10) cc_final: 0.8495 (m-80) REVERT: C 453 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8607 (mm-30) REVERT: C 475 ARG cc_start: 0.8401 (ttp80) cc_final: 0.7801 (ttp80) REVERT: C 482 TRP cc_start: 0.8353 (m-90) cc_final: 0.7773 (m-90) REVERT: C 518 MET cc_start: 0.8025 (ttm) cc_final: 0.7699 (mtt) REVERT: C 525 MET cc_start: 0.7862 (ttm) cc_final: 0.7268 (tmm) REVERT: C 541 ASP cc_start: 0.8500 (m-30) cc_final: 0.8256 (m-30) REVERT: C 645 PHE cc_start: 0.8442 (t80) cc_final: 0.8032 (t80) REVERT: C 685 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8569 (mmmt) REVERT: C 692 MET cc_start: 0.8361 (ptp) cc_final: 0.7911 (ptp) REVERT: C 727 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: C 735 GLU cc_start: 0.8516 (tt0) cc_final: 0.8205 (pt0) REVERT: C 736 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.8030 (pt0) REVERT: C 783 LYS cc_start: 0.8631 (tttt) cc_final: 0.8203 (tptt) REVERT: C 807 SER cc_start: 0.8058 (p) cc_final: 0.7813 (t) REVERT: D 453 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6690 (mm-30) REVERT: D 485 MET cc_start: 0.6890 (mmm) cc_final: 0.6332 (mmt) REVERT: D 513 PHE cc_start: 0.8566 (m-80) cc_final: 0.8295 (m-80) REVERT: D 530 GLN cc_start: 0.8436 (tp40) cc_final: 0.8131 (mm-40) REVERT: D 533 LYS cc_start: 0.7848 (mptt) cc_final: 0.7193 (mttm) REVERT: D 541 ASP cc_start: 0.8374 (m-30) cc_final: 0.7919 (t0) REVERT: D 676 SER cc_start: 0.8852 (t) cc_final: 0.8311 (m) REVERT: D 692 MET cc_start: 0.9000 (mtp) cc_final: 0.8491 (mmm) REVERT: D 732 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7963 (tt0) REVERT: D 786 ASN cc_start: 0.8655 (m-40) cc_final: 0.8354 (m110) REVERT: H 10 MET cc_start: 0.8580 (tpp) cc_final: 0.8336 (mmm) REVERT: H 24 MET cc_start: 0.8587 (tpt) cc_final: 0.8300 (tpt) REVERT: H 79 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: F 78 LYS cc_start: 0.7591 (pttt) cc_final: 0.7189 (ptpt) REVERT: G 120 LEU cc_start: 0.7942 (tt) cc_final: 0.7678 (mp) REVERT: G 131 ARG cc_start: 0.7615 (ttt180) cc_final: 0.6957 (mmm160) REVERT: E 37 ARG cc_start: 0.7177 (mmp80) cc_final: 0.6933 (mmp80) REVERT: E 149 ASN cc_start: 0.8712 (t0) cc_final: 0.8261 (t0) REVERT: E 203 ASP cc_start: 0.8214 (t0) cc_final: 0.7779 (t70) outliers start: 43 outliers final: 23 residues processed: 377 average time/residue: 0.1470 time to fit residues: 82.9373 Evaluate side-chains 358 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 740 CYS Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 204 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 184 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 457 HIS C 736 GLN D 608 GLN ** H 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS E 205 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.188500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117796 restraints weight = 22721.164| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.89 r_work: 0.3255 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18526 Z= 0.218 Angle : 0.631 8.938 25040 Z= 0.326 Chirality : 0.044 0.172 2800 Planarity : 0.004 0.046 3056 Dihedral : 7.256 79.367 2596 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.01 % Favored : 96.85 % Rotamer: Outliers : 2.81 % Allowed : 16.48 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.68 (0.18), residues: 2256 helix: 1.68 (0.15), residues: 1289 sheet: -1.38 (0.38), residues: 152 loop : -1.19 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 507 TYR 0.019 0.002 TYR A 427 PHE 0.030 0.002 PHE C 563 TRP 0.028 0.002 TRP G 178 HIS 0.008 0.002 HIS E 205 Details of bonding type rmsd covalent geometry : bond 0.00540 (18516) covalent geometry : angle 0.62803 (25020) SS BOND : bond 0.00615 ( 10) SS BOND : angle 2.08170 ( 20) hydrogen bonds : bond 0.04127 ( 1040) hydrogen bonds : angle 4.13927 ( 2979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 347 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5892 (OUTLIER) cc_final: 0.5539 (p0) REVERT: A 485 MET cc_start: 0.9321 (mtp) cc_final: 0.8571 (mmt) REVERT: A 567 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8078 (mtt90) REVERT: A 666 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 690 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7796 (mp0) REVERT: A 710 GLU cc_start: 0.8196 (tt0) cc_final: 0.7858 (tt0) REVERT: A 833 LEU cc_start: 0.7670 (tt) cc_final: 0.7234 (mm) REVERT: B 441 ASP cc_start: 0.8203 (m-30) cc_final: 0.7761 (t70) REVERT: B 491 TYR cc_start: 0.8215 (m-80) cc_final: 0.7842 (m-80) REVERT: B 508 GLU cc_start: 0.8446 (tp30) cc_final: 0.7625 (tp30) REVERT: B 511 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7516 (tt) REVERT: B 567 ARG cc_start: 0.6824 (mtt90) cc_final: 0.3992 (mtt180) REVERT: B 678 LYS cc_start: 0.8053 (tttt) cc_final: 0.7684 (tttt) REVERT: B 692 MET cc_start: 0.9149 (mtm) cc_final: 0.8651 (mtm) REVERT: B 696 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: B 704 PHE cc_start: 0.8633 (m-80) cc_final: 0.8015 (m-80) REVERT: B 738 LYS cc_start: 0.8970 (mtpt) cc_final: 0.8361 (mmmt) REVERT: B 782 ASP cc_start: 0.8837 (m-30) cc_final: 0.8221 (t70) REVERT: B 786 ASN cc_start: 0.8451 (m-40) cc_final: 0.7900 (m110) REVERT: B 819 TYR cc_start: 0.8946 (m-10) cc_final: 0.8572 (m-80) REVERT: C 453 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8664 (mm-30) REVERT: C 472 TYR cc_start: 0.8475 (m-80) cc_final: 0.8274 (m-80) REVERT: C 475 ARG cc_start: 0.8475 (ttp80) cc_final: 0.7894 (ttp80) REVERT: C 482 TRP cc_start: 0.8360 (m-90) cc_final: 0.7794 (m-90) REVERT: C 525 MET cc_start: 0.7985 (ttm) cc_final: 0.7674 (ttp) REVERT: C 541 ASP cc_start: 0.8454 (m-30) cc_final: 0.8249 (m-30) REVERT: C 645 PHE cc_start: 0.8549 (t80) cc_final: 0.8121 (t80) REVERT: C 692 MET cc_start: 0.8364 (ptp) cc_final: 0.7937 (ptp) REVERT: C 727 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6883 (mt-10) REVERT: C 735 GLU cc_start: 0.8416 (tt0) cc_final: 0.8079 (pt0) REVERT: C 783 LYS cc_start: 0.8657 (tttt) cc_final: 0.8207 (tptt) REVERT: D 453 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6884 (mm-30) REVERT: D 513 PHE cc_start: 0.8619 (m-80) cc_final: 0.8399 (m-80) REVERT: D 530 GLN cc_start: 0.8443 (tp40) cc_final: 0.8123 (mm-40) REVERT: D 533 LYS cc_start: 0.7857 (mptt) cc_final: 0.7204 (mttm) REVERT: D 541 ASP cc_start: 0.8414 (m-30) cc_final: 0.8008 (t0) REVERT: D 676 SER cc_start: 0.8930 (t) cc_final: 0.8334 (m) REVERT: D 692 MET cc_start: 0.9058 (mtp) cc_final: 0.8617 (mmm) REVERT: D 786 ASN cc_start: 0.8696 (m-40) cc_final: 0.8354 (m110) REVERT: H 10 MET cc_start: 0.8674 (tpp) cc_final: 0.8404 (mmm) REVERT: H 37 ARG cc_start: 0.8078 (tmt170) cc_final: 0.7875 (tmt170) REVERT: H 79 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: F 24 MET cc_start: 0.7798 (tpp) cc_final: 0.7521 (tpp) REVERT: G 120 LEU cc_start: 0.8027 (tt) cc_final: 0.7724 (mp) REVERT: E 149 ASN cc_start: 0.8766 (t0) cc_final: 0.8365 (t0) REVERT: E 203 ASP cc_start: 0.8229 (t0) cc_final: 0.7797 (t70) outliers start: 54 outliers final: 36 residues processed: 383 average time/residue: 0.1485 time to fit residues: 85.1603 Evaluate side-chains 367 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 750 ASP Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 113 optimal weight: 0.8980 chunk 209 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN D 608 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.203931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.130020 restraints weight = 23476.267| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.56 r_work: 0.3532 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18526 Z= 0.150 Angle : 0.591 9.098 25040 Z= 0.302 Chirality : 0.042 0.209 2800 Planarity : 0.004 0.042 3056 Dihedral : 6.735 79.274 2596 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.93 % Favored : 96.94 % Rotamer: Outliers : 2.18 % Allowed : 17.67 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.83 (0.18), residues: 2256 helix: 1.85 (0.15), residues: 1282 sheet: -1.30 (0.38), residues: 159 loop : -1.20 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 37 TYR 0.016 0.001 TYR A 427 PHE 0.015 0.001 PHE B 836 TRP 0.024 0.001 TRP G 178 HIS 0.015 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00364 (18516) covalent geometry : angle 0.58756 (25020) SS BOND : bond 0.00465 ( 10) SS BOND : angle 2.22895 ( 20) hydrogen bonds : bond 0.03788 ( 1040) hydrogen bonds : angle 4.01645 ( 2979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 348 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5897 (OUTLIER) cc_final: 0.5533 (p0) REVERT: A 442 LYS cc_start: 0.8225 (tttt) cc_final: 0.7903 (mtpp) REVERT: A 485 MET cc_start: 0.9290 (mtp) cc_final: 0.8613 (mmt) REVERT: A 567 ARG cc_start: 0.8636 (mtp180) cc_final: 0.7951 (mtt90) REVERT: A 690 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7720 (mp0) REVERT: A 692 MET cc_start: 0.8796 (mpp) cc_final: 0.8498 (mpp) REVERT: A 710 GLU cc_start: 0.8188 (tt0) cc_final: 0.7861 (tt0) REVERT: A 833 LEU cc_start: 0.7757 (tt) cc_final: 0.7373 (mm) REVERT: B 441 ASP cc_start: 0.8131 (m-30) cc_final: 0.7893 (t0) REVERT: B 491 TYR cc_start: 0.8219 (m-80) cc_final: 0.7825 (m-80) REVERT: B 508 GLU cc_start: 0.8476 (tp30) cc_final: 0.7673 (tp30) REVERT: B 567 ARG cc_start: 0.6974 (mtt90) cc_final: 0.4192 (mtt180) REVERT: B 678 LYS cc_start: 0.8105 (tttt) cc_final: 0.7796 (tttt) REVERT: B 692 MET cc_start: 0.9131 (mtm) cc_final: 0.8729 (mtm) REVERT: B 696 MET cc_start: 0.8805 (mtm) cc_final: 0.8260 (mtm) REVERT: B 738 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8457 (mmmt) REVERT: B 782 ASP cc_start: 0.8743 (m-30) cc_final: 0.8209 (t70) REVERT: B 786 ASN cc_start: 0.8431 (m-40) cc_final: 0.7900 (m-40) REVERT: B 819 TYR cc_start: 0.8971 (m-10) cc_final: 0.8576 (m-80) REVERT: C 453 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 475 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8072 (ttp80) REVERT: C 482 TRP cc_start: 0.8295 (m-90) cc_final: 0.7747 (m-90) REVERT: C 518 MET cc_start: 0.8245 (ttm) cc_final: 0.7826 (mtt) REVERT: C 525 MET cc_start: 0.8100 (ttm) cc_final: 0.7533 (tmm) REVERT: C 645 PHE cc_start: 0.8657 (t80) cc_final: 0.8254 (t80) REVERT: C 692 MET cc_start: 0.8412 (ptp) cc_final: 0.7991 (ptp) REVERT: C 727 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: C 735 GLU cc_start: 0.8451 (tt0) cc_final: 0.8207 (pt0) REVERT: C 783 LYS cc_start: 0.8598 (tttt) cc_final: 0.8122 (tptt) REVERT: C 788 TRP cc_start: 0.8818 (m100) cc_final: 0.8104 (m100) REVERT: D 453 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6889 (mm-30) REVERT: D 482 TRP cc_start: 0.8001 (m100) cc_final: 0.7252 (m100) REVERT: D 530 GLN cc_start: 0.8489 (tp40) cc_final: 0.8203 (mm-40) REVERT: D 533 LYS cc_start: 0.7843 (mptt) cc_final: 0.7219 (mttm) REVERT: D 541 ASP cc_start: 0.8286 (m-30) cc_final: 0.7939 (t0) REVERT: D 676 SER cc_start: 0.8969 (t) cc_final: 0.8428 (m) REVERT: D 692 MET cc_start: 0.8943 (mtp) cc_final: 0.8596 (mmm) REVERT: D 710 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7679 (pt0) REVERT: D 786 ASN cc_start: 0.8716 (m-40) cc_final: 0.8374 (m110) REVERT: H 10 MET cc_start: 0.8706 (tpp) cc_final: 0.8471 (mmm) REVERT: H 24 MET cc_start: 0.8708 (tpt) cc_final: 0.8429 (tpt) REVERT: H 37 ARG cc_start: 0.8179 (tmt170) cc_final: 0.7964 (tmt170) REVERT: H 79 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: F 24 MET cc_start: 0.7933 (tpp) cc_final: 0.7730 (tpp) REVERT: G 120 LEU cc_start: 0.8051 (tt) cc_final: 0.7763 (mp) REVERT: G 129 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (mttp) REVERT: E 149 ASN cc_start: 0.8827 (t0) cc_final: 0.8409 (t0) REVERT: E 203 ASP cc_start: 0.8255 (t0) cc_final: 0.7918 (t70) outliers start: 42 outliers final: 30 residues processed: 379 average time/residue: 0.1489 time to fit residues: 84.1761 Evaluate side-chains 362 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 328 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 180 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN D 608 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.204091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130441 restraints weight = 23476.983| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.56 r_work: 0.3540 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18526 Z= 0.141 Angle : 0.581 8.763 25040 Z= 0.298 Chirality : 0.042 0.221 2800 Planarity : 0.004 0.044 3056 Dihedral : 6.244 79.206 2596 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.97 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 18.61 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 0.95 (0.18), residues: 2256 helix: 1.92 (0.15), residues: 1283 sheet: -1.35 (0.39), residues: 147 loop : -1.09 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 37 TYR 0.013 0.001 TYR G 96 PHE 0.014 0.001 PHE B 836 TRP 0.023 0.001 TRP G 178 HIS 0.016 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00337 (18516) covalent geometry : angle 0.57824 (25020) SS BOND : bond 0.00553 ( 10) SS BOND : angle 2.11502 ( 20) hydrogen bonds : bond 0.03679 ( 1040) hydrogen bonds : angle 3.98087 ( 2979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 341 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 ASN cc_start: 0.5965 (OUTLIER) cc_final: 0.5600 (p0) REVERT: A 442 LYS cc_start: 0.8249 (tttt) cc_final: 0.7962 (mtpp) REVERT: A 485 MET cc_start: 0.9291 (mtp) cc_final: 0.8616 (mmt) REVERT: A 567 ARG cc_start: 0.8630 (mtp180) cc_final: 0.7931 (mtt90) REVERT: A 672 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7016 (tt) REVERT: A 690 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7697 (mp0) REVERT: A 710 GLU cc_start: 0.8203 (tt0) cc_final: 0.7863 (tt0) REVERT: A 833 LEU cc_start: 0.7635 (tt) cc_final: 0.7279 (mm) REVERT: B 440 ASN cc_start: 0.7808 (m-40) cc_final: 0.7475 (m-40) REVERT: B 441 ASP cc_start: 0.8145 (m-30) cc_final: 0.7922 (t0) REVERT: B 491 TYR cc_start: 0.8256 (m-80) cc_final: 0.7820 (m-80) REVERT: B 567 ARG cc_start: 0.6872 (mtt90) cc_final: 0.4242 (mtt180) REVERT: B 678 LYS cc_start: 0.8118 (tttt) cc_final: 0.7803 (tttt) REVERT: B 692 MET cc_start: 0.9156 (mtm) cc_final: 0.8734 (mtm) REVERT: B 696 MET cc_start: 0.8798 (mtm) cc_final: 0.8279 (mtm) REVERT: B 738 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8465 (mmmt) REVERT: B 782 ASP cc_start: 0.8724 (m-30) cc_final: 0.8153 (t70) REVERT: B 786 ASN cc_start: 0.8430 (m-40) cc_final: 0.8033 (m-40) REVERT: B 819 TYR cc_start: 0.8953 (m-10) cc_final: 0.8561 (m-80) REVERT: C 453 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8586 (mm-30) REVERT: C 475 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8035 (ttp80) REVERT: C 482 TRP cc_start: 0.8272 (m-90) cc_final: 0.7802 (m-90) REVERT: C 518 MET cc_start: 0.8239 (ttm) cc_final: 0.7960 (mtt) REVERT: C 525 MET cc_start: 0.8070 (ttm) cc_final: 0.7511 (tmm) REVERT: C 645 PHE cc_start: 0.8668 (t80) cc_final: 0.8346 (t80) REVERT: C 692 MET cc_start: 0.8406 (ptp) cc_final: 0.8003 (ptp) REVERT: C 727 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: C 735 GLU cc_start: 0.8469 (tt0) cc_final: 0.8170 (pt0) REVERT: C 736 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7528 (pp30) REVERT: C 783 LYS cc_start: 0.8605 (tttt) cc_final: 0.8135 (tptt) REVERT: C 788 TRP cc_start: 0.8828 (m100) cc_final: 0.8087 (m100) REVERT: D 453 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6933 (mm-30) REVERT: D 485 MET cc_start: 0.6916 (mmm) cc_final: 0.6525 (mmt) REVERT: D 530 GLN cc_start: 0.8529 (tp40) cc_final: 0.8228 (mm-40) REVERT: D 533 LYS cc_start: 0.7879 (mptt) cc_final: 0.7267 (mttm) REVERT: D 541 ASP cc_start: 0.8309 (m-30) cc_final: 0.7929 (t0) REVERT: D 676 SER cc_start: 0.8953 (t) cc_final: 0.8398 (m) REVERT: D 692 MET cc_start: 0.8970 (mtp) cc_final: 0.8587 (mmm) REVERT: D 710 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7659 (pt0) REVERT: D 786 ASN cc_start: 0.8664 (m-40) cc_final: 0.8350 (m110) REVERT: H 10 MET cc_start: 0.8679 (tpp) cc_final: 0.8450 (mmm) REVERT: H 24 MET cc_start: 0.8698 (tpt) cc_final: 0.8396 (tpt) REVERT: H 37 ARG cc_start: 0.8181 (tmt170) cc_final: 0.7969 (tmt170) REVERT: H 79 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8006 (mp10) REVERT: G 120 LEU cc_start: 0.8077 (tt) cc_final: 0.7753 (mp) REVERT: G 129 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8303 (mttp) REVERT: E 149 ASN cc_start: 0.8808 (t0) cc_final: 0.8370 (t0) outliers start: 39 outliers final: 29 residues processed: 370 average time/residue: 0.1461 time to fit residues: 80.9690 Evaluate side-chains 358 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 511 ILE Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 740 CYS Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN D 608 GLN ** D 769 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.205190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.131648 restraints weight = 23296.112| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.56 r_work: 0.3551 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18526 Z= 0.131 Angle : 0.579 9.146 25040 Z= 0.296 Chirality : 0.042 0.197 2800 Planarity : 0.004 0.042 3056 Dihedral : 5.986 74.105 2596 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.88 % Favored : 96.99 % Rotamer: Outliers : 1.82 % Allowed : 19.28 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.03 (0.19), residues: 2256 helix: 1.98 (0.15), residues: 1283 sheet: -1.36 (0.40), residues: 147 loop : -1.03 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 737 TYR 0.025 0.001 TYR C 472 PHE 0.013 0.001 PHE D 836 TRP 0.021 0.001 TRP G 178 HIS 0.014 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00308 (18516) covalent geometry : angle 0.57627 (25020) SS BOND : bond 0.00504 ( 10) SS BOND : angle 2.03853 ( 20) hydrogen bonds : bond 0.03598 ( 1040) hydrogen bonds : angle 3.95230 ( 2979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 331 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8268 (tttt) cc_final: 0.7997 (mtpp) REVERT: A 485 MET cc_start: 0.9273 (mtp) cc_final: 0.8594 (mmt) REVERT: A 567 ARG cc_start: 0.8637 (mtp180) cc_final: 0.7926 (mtt90) REVERT: A 666 GLU cc_start: 0.8637 (tp30) cc_final: 0.8316 (tm-30) REVERT: A 672 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6963 (tt) REVERT: A 690 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7693 (mp0) REVERT: A 692 MET cc_start: 0.8720 (mpp) cc_final: 0.8433 (mpp) REVERT: A 710 GLU cc_start: 0.8198 (tt0) cc_final: 0.7883 (tt0) REVERT: A 833 LEU cc_start: 0.7641 (tt) cc_final: 0.7313 (mm) REVERT: B 441 ASP cc_start: 0.8137 (m-30) cc_final: 0.7897 (t0) REVERT: B 485 MET cc_start: 0.9153 (mtm) cc_final: 0.8662 (mmm) REVERT: B 491 TYR cc_start: 0.8273 (m-80) cc_final: 0.7866 (m-80) REVERT: B 567 ARG cc_start: 0.6875 (mtt90) cc_final: 0.4236 (mtt180) REVERT: B 667 ILE cc_start: 0.7667 (mt) cc_final: 0.7400 (mm) REVERT: B 678 LYS cc_start: 0.8110 (tttt) cc_final: 0.7807 (tttt) REVERT: B 738 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8481 (mmmt) REVERT: B 782 ASP cc_start: 0.8733 (m-30) cc_final: 0.8127 (t70) REVERT: B 786 ASN cc_start: 0.8435 (m-40) cc_final: 0.8061 (m110) REVERT: B 819 TYR cc_start: 0.8935 (m-10) cc_final: 0.8557 (m-80) REVERT: C 453 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8591 (mm-30) REVERT: C 472 TYR cc_start: 0.7973 (m-80) cc_final: 0.7706 (m-10) REVERT: C 475 ARG cc_start: 0.8499 (ttp80) cc_final: 0.7944 (ttp80) REVERT: C 482 TRP cc_start: 0.8286 (m-90) cc_final: 0.7840 (m-90) REVERT: C 518 MET cc_start: 0.8239 (ttm) cc_final: 0.7986 (mtt) REVERT: C 525 MET cc_start: 0.8059 (ttm) cc_final: 0.7520 (tmm) REVERT: C 645 PHE cc_start: 0.8657 (t80) cc_final: 0.8351 (t80) REVERT: C 692 MET cc_start: 0.8370 (ptp) cc_final: 0.7947 (ptp) REVERT: C 727 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6762 (mt-10) REVERT: C 735 GLU cc_start: 0.8474 (tt0) cc_final: 0.8183 (pt0) REVERT: C 736 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7390 (pp30) REVERT: C 783 LYS cc_start: 0.8595 (tttt) cc_final: 0.8113 (tptt) REVERT: C 788 TRP cc_start: 0.8795 (m100) cc_final: 0.8141 (m100) REVERT: D 453 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6951 (mm-30) REVERT: D 530 GLN cc_start: 0.8541 (tp40) cc_final: 0.8241 (mm-40) REVERT: D 533 LYS cc_start: 0.7854 (mptt) cc_final: 0.7266 (mttm) REVERT: D 541 ASP cc_start: 0.8290 (m-30) cc_final: 0.7906 (t0) REVERT: D 676 SER cc_start: 0.8941 (t) cc_final: 0.8396 (m) REVERT: D 682 ARG cc_start: 0.7956 (mtt180) cc_final: 0.7497 (ttm-80) REVERT: D 692 MET cc_start: 0.8955 (mtp) cc_final: 0.8541 (mmm) REVERT: D 710 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7642 (pt0) REVERT: D 786 ASN cc_start: 0.8681 (m-40) cc_final: 0.8353 (m110) REVERT: H 24 MET cc_start: 0.8715 (tpt) cc_final: 0.8448 (tpt) REVERT: H 79 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: F 117 MET cc_start: 0.9139 (mmm) cc_final: 0.8920 (mmt) REVERT: G 120 LEU cc_start: 0.8001 (tt) cc_final: 0.7659 (mp) REVERT: G 129 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8290 (mttp) REVERT: E 149 ASN cc_start: 0.8795 (t0) cc_final: 0.8354 (t0) outliers start: 35 outliers final: 28 residues processed: 357 average time/residue: 0.1462 time to fit residues: 78.0741 Evaluate side-chains 358 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 325 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain C residue 736 GLN Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 199 HIS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 201 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 216 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 736 GLN D 608 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.205109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137158 restraints weight = 23291.024| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.15 r_work: 0.3517 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18526 Z= 0.137 Angle : 0.585 10.100 25040 Z= 0.298 Chirality : 0.042 0.214 2800 Planarity : 0.004 0.045 3056 Dihedral : 5.825 72.082 2596 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.15 % Favored : 96.72 % Rotamer: Outliers : 1.72 % Allowed : 19.28 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: 1.06 (0.19), residues: 2256 helix: 2.00 (0.15), residues: 1284 sheet: -1.29 (0.39), residues: 159 loop : -1.02 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 37 TYR 0.022 0.001 TYR C 472 PHE 0.013 0.001 PHE D 836 TRP 0.021 0.001 TRP G 178 HIS 0.014 0.001 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00326 (18516) covalent geometry : angle 0.58162 (25020) SS BOND : bond 0.00750 ( 10) SS BOND : angle 2.20739 ( 20) hydrogen bonds : bond 0.03616 ( 1040) hydrogen bonds : angle 3.95709 ( 2979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 LYS cc_start: 0.8250 (tttt) cc_final: 0.8012 (mtpp) REVERT: A 567 ARG cc_start: 0.8570 (mtp180) cc_final: 0.7873 (mtt90) REVERT: A 666 GLU cc_start: 0.8594 (tp30) cc_final: 0.8295 (tm-30) REVERT: A 672 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6804 (tt) REVERT: A 690 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7662 (mp0) REVERT: A 710 GLU cc_start: 0.8178 (tt0) cc_final: 0.7864 (tt0) REVERT: A 743 MET cc_start: 0.7699 (ppp) cc_final: 0.7217 (ppp) REVERT: A 833 LEU cc_start: 0.7624 (tt) cc_final: 0.7321 (mm) REVERT: B 440 ASN cc_start: 0.7850 (m-40) cc_final: 0.7582 (m-40) REVERT: B 441 ASP cc_start: 0.8153 (m-30) cc_final: 0.7937 (t0) REVERT: B 485 MET cc_start: 0.9143 (mtm) cc_final: 0.8663 (mmm) REVERT: B 491 TYR cc_start: 0.8293 (m-80) cc_final: 0.7948 (m-80) REVERT: B 567 ARG cc_start: 0.6677 (mtt90) cc_final: 0.4244 (mtt180) REVERT: B 667 ILE cc_start: 0.7637 (mt) cc_final: 0.7376 (mm) REVERT: B 678 LYS cc_start: 0.8115 (tttt) cc_final: 0.7699 (tttt) REVERT: B 704 PHE cc_start: 0.8671 (m-80) cc_final: 0.7921 (m-80) REVERT: B 738 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8465 (mmmt) REVERT: B 782 ASP cc_start: 0.8702 (m-30) cc_final: 0.8104 (t70) REVERT: B 786 ASN cc_start: 0.8399 (m-40) cc_final: 0.8026 (m110) REVERT: B 819 TYR cc_start: 0.8878 (m-10) cc_final: 0.8508 (m-80) REVERT: C 453 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 518 MET cc_start: 0.8163 (ttm) cc_final: 0.7896 (mtt) REVERT: C 525 MET cc_start: 0.8050 (ttm) cc_final: 0.7488 (tmm) REVERT: C 645 PHE cc_start: 0.8634 (t80) cc_final: 0.8371 (t80) REVERT: C 692 MET cc_start: 0.8319 (ptp) cc_final: 0.7926 (ptp) REVERT: C 727 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: C 735 GLU cc_start: 0.8415 (tt0) cc_final: 0.8125 (pt0) REVERT: C 783 LYS cc_start: 0.8608 (tttt) cc_final: 0.8123 (tptt) REVERT: D 453 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6933 (mm-30) REVERT: D 485 MET cc_start: 0.6700 (mmm) cc_final: 0.6336 (mmt) REVERT: D 530 GLN cc_start: 0.8532 (tp40) cc_final: 0.8239 (mm-40) REVERT: D 533 LYS cc_start: 0.7848 (mptt) cc_final: 0.7303 (mttm) REVERT: D 541 ASP cc_start: 0.8145 (m-30) cc_final: 0.7852 (t0) REVERT: D 676 SER cc_start: 0.8938 (t) cc_final: 0.8382 (m) REVERT: D 692 MET cc_start: 0.8877 (mtp) cc_final: 0.8476 (mmm) REVERT: D 710 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7613 (pt0) REVERT: D 786 ASN cc_start: 0.8686 (m-40) cc_final: 0.8349 (m110) REVERT: H 24 MET cc_start: 0.8658 (tpt) cc_final: 0.8381 (tpt) REVERT: H 79 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: F 117 MET cc_start: 0.9119 (mmm) cc_final: 0.8843 (mmt) REVERT: G 120 LEU cc_start: 0.8032 (tt) cc_final: 0.7692 (mp) REVERT: G 129 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (mttp) REVERT: E 10 MET cc_start: 0.8533 (mmm) cc_final: 0.8250 (mmm) REVERT: E 37 ARG cc_start: 0.6887 (mmp80) cc_final: 0.5684 (mmp80) REVERT: E 149 ASN cc_start: 0.8731 (t0) cc_final: 0.8307 (t0) outliers start: 33 outliers final: 26 residues processed: 353 average time/residue: 0.1447 time to fit residues: 76.0262 Evaluate side-chains 350 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 320 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 493 LYS Chi-restraints excluded: chain A residue 502 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 688 VAL Chi-restraints excluded: chain B residue 837 CYS Chi-restraints excluded: chain C residue 563 PHE Chi-restraints excluded: chain C residue 727 GLU Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 715 VAL Chi-restraints excluded: chain D residue 795 CYS Chi-restraints excluded: chain D residue 817 VAL Chi-restraints excluded: chain D residue 840 SER Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 211 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: ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN D 608 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.201607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.127298 restraints weight = 23634.804| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.55 r_work: 0.3529 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18526 Z= 0.218 Angle : 0.640 10.226 25040 Z= 0.331 Chirality : 0.044 0.181 2800 Planarity : 0.004 0.046 3056 Dihedral : 5.882 73.318 2596 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer: Outliers : 1.92 % Allowed : 19.39 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.79 (0.18), residues: 2256 helix: 1.75 (0.15), residues: 1283 sheet: -1.29 (0.39), residues: 159 loop : -1.08 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 697 TYR 0.026 0.002 TYR C 472 PHE 0.015 0.001 PHE A 630 TRP 0.034 0.002 TRP C 482 HIS 0.027 0.002 HIS F 205 Details of bonding type rmsd covalent geometry : bond 0.00539 (18516) covalent geometry : angle 0.63680 (25020) SS BOND : bond 0.00503 ( 10) SS BOND : angle 2.41298 ( 20) hydrogen bonds : bond 0.04093 ( 1040) hydrogen bonds : angle 4.14421 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6294.70 seconds wall clock time: 108 minutes 16.60 seconds (6496.60 seconds total)