Starting phenix.real_space_refine on Thu Feb 5 15:44:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p9d_71407/02_2026/9p9d_71407.map" } resolution = 3.82 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= 0.014 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 3 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': 2, 'PTRANS': 13, '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: 4.59, per 1000 atoms: 0.25 Number of scatterers: 18100 At special positions: 0 Unit cell: (129.27, 111.6, 135.78, 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=11, symmetry=0 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 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: 1.76 Conformation dependent library (CDL) restraints added in 814.3 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: 95 helices and 23 sheets defined 58.8% alpha, 8.1% 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 504 through 509 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.859A pdb=" N TRP A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 568 removed outlier: 3.588A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.837A pdb=" N SER A 598 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 646 Processing helix chain 'A' and resid 657 through 664 Processing helix chain 'A' and resid 675 through 683 Processing helix chain 'A' and resid 686 through 697 Processing helix chain 'A' and resid 707 through 718 Processing helix chain 'A' and resid 728 through 737 Processing helix chain 'A' and resid 764 through 778 Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 840 removed outlier: 3.611A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (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 537 through 541 Processing helix chain 'B' and resid 544 through 568 Processing helix chain 'B' and resid 594 through 607 removed outlier: 3.546A pdb=" N SER B 598 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 640 removed outlier: 3.638A pdb=" N VAL B 623 " --> pdb=" O SER B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 Processing helix chain 'B' and resid 657 through 663 Processing helix chain 'B' and resid 675 through 684 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 736 Processing helix chain 'B' and resid 764 through 778 Processing helix chain 'B' and resid 779 through 789 Processing helix chain 'B' and resid 810 through 813 Processing helix chain 'B' and resid 814 through 839 removed outlier: 3.547A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 441 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 Processing helix chain 'C' and resid 594 through 607 Processing helix chain 'C' and resid 617 through 646 removed outlier: 3.568A pdb=" N ALA C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 664 Processing helix chain 'C' and resid 675 through 683 Processing helix chain 'C' and resid 686 through 699 Processing helix chain 'C' and resid 707 through 719 removed outlier: 3.677A pdb=" N LYS C 719 " --> pdb=" O VAL C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 764 through 778 Processing helix chain 'C' and resid 779 through 789 Processing helix chain 'C' and resid 790 through 793 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 840 removed outlier: 3.807A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 839 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 840 " --> pdb=" O PHE C 836 " (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 Processing helix chain 'D' and resid 483 through 491 Processing helix chain 'D' and resid 504 through 509 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 544 through 568 Processing helix chain 'D' and resid 594 through 607 Processing helix chain 'D' and resid 617 through 640 Processing helix chain 'D' and resid 641 through 645 Processing helix chain 'D' and resid 657 through 663 Processing helix chain 'D' and resid 675 through 684 Processing helix chain 'D' and resid 686 through 699 Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 728 through 737 Processing helix chain 'D' and resid 764 through 778 Processing helix chain 'D' and resid 779 through 790 removed outlier: 3.560A pdb=" N LYS D 787 " --> pdb=" O LYS D 783 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 788 " --> pdb=" O LEU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 800 Processing helix chain 'D' and resid 810 through 839 removed outlier: 3.884A pdb=" N VAL D 814 " --> pdb=" O SER D 810 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY D 816 " --> pdb=" O SER D 812 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 817 " --> pdb=" O ASN D 813 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU D 830 " --> pdb=" O GLY D 826 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 29 removed outlier: 4.046A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 18 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 105 removed outlier: 3.907A pdb=" N ARG H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 125 Processing helix chain 'H' and resid 132 through 161 removed outlier: 3.787A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 208 removed outlier: 3.501A pdb=" N TYR H 181 " --> pdb=" O GLY H 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 95 through 105 Processing helix chain 'F' and resid 105 through 125 Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.956A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 207 removed outlier: 3.734A pdb=" N TYR F 181 " --> pdb=" O GLY F 177 " (cutoff:3.500A) 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 7 through 29 Processing helix chain 'G' and resid 95 through 105 Processing helix chain 'G' and resid 105 through 127 Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.672A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 207 removed outlier: 3.775A 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 125 removed outlier: 3.988A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 160 Processing helix chain 'E' and resid 177 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 466 removed outlier: 6.353A pdb=" N VAL A 417 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ALA A 465 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 419 " --> pdb=" O ALA A 465 " (cutoff:3.500A) 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 520 removed outlier: 4.716A pdb=" N VAL A 756 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TYR A 754 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N MET A 518 " --> pdb=" O LYS A 752 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 752 " --> pdb=" O MET A 518 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 670 removed outlier: 6.504A pdb=" N ALA A 668 " --> pdb=" O ALA A 723 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N LEU A 725 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY A 670 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU A 727 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 8.921A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 417 through 421 Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 430 Processing sheet with id=AA7, first strand: chain 'B' and resid 511 through 512 Processing sheet with id=AA8, first strand: chain 'B' and resid 518 through 520 removed outlier: 4.006A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 724 through 727 removed outlier: 3.871A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 462 through 466 Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AB3, first strand: chain 'C' and resid 511 through 513 Processing sheet with id=AB4, first strand: chain 'C' and resid 518 through 520 removed outlier: 3.856A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 668 through 670 removed outlier: 6.251A pdb=" N ALA C 668 " --> pdb=" O ALA C 723 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 725 " --> pdb=" O ALA C 668 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 670 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N GLU C 727 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 9.143A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 462 through 466 removed outlier: 6.857A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA D 465 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 419 " --> pdb=" O ALA D 465 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 496 " --> pdb=" O VAL D 418 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 430 Processing sheet with id=AB8, first strand: chain 'D' and resid 511 through 513 Processing sheet with id=AB9, first strand: chain 'D' and resid 518 through 520 removed outlier: 3.909A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.637A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AC3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AC4, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.517A pdb=" N SER G 175 " --> pdb=" O TYR G 35 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 78 through 79 1077 hydrogen bonds defined for protein. 3087 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: 3.54 Time building geometry restraints manager: 2.27 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: 7879 1.52 - 1.68: 4877 1.68 - 1.85: 220 Bond restraints: 18516 Sorted by residual: bond pdb=" C4 CYZ A 902 " pdb=" C5 CYZ A 902 " ideal model delta sigma weight residual 1.512 1.031 0.481 2.00e-02 2.50e+03 5.78e+02 bond pdb=" C4 CYZ C 902 " pdb=" C5 CYZ C 902 " ideal model delta sigma weight residual 1.512 1.032 0.480 2.00e-02 2.50e+03 5.76e+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 5.76e+02 bond pdb=" C4 CYZ B 902 " pdb=" C5 CYZ B 902 " ideal model delta sigma weight residual 1.512 1.033 0.479 2.00e-02 2.50e+03 5.74e+02 bond pdb=" C5 CYZ D 902 " pdb=" C6 CYZ D 902 " ideal model delta sigma weight residual 1.553 1.075 0.478 2.00e-02 2.50e+03 5.72e+02 ... (remaining 18511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 24899 4.28 - 8.56: 99 8.56 - 12.83: 6 12.83 - 17.11: 11 17.11 - 21.39: 5 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 106.92 128.31 -21.39 3.00e+00 1.11e-01 5.08e+01 angle pdb=" C1 CYZ C 902 " pdb=" C2 CYZ C 902 " pdb=" C3 CYZ C 902 " ideal model delta sigma weight residual 106.92 128.27 -21.35 3.00e+00 1.11e-01 5.06e+01 angle pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C3 CYZ D 902 " ideal model delta sigma weight residual 106.92 128.27 -21.35 3.00e+00 1.11e-01 5.06e+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=" O3 CYZ B 902 " pdb=" S2 CYZ B 902 " pdb=" O4 CYZ B 902 " ideal model delta sigma weight residual 118.35 101.18 17.17 3.00e+00 1.11e-01 3.28e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 10456 22.99 - 45.98: 385 45.98 - 68.97: 36 68.97 - 91.96: 27 91.96 - 114.95: 9 Dihedral angle restraints: 10913 sinusoidal: 4317 harmonic: 6596 Sorted by residual: dihedral pdb=" CA TRP C 789 " pdb=" C TRP C 789 " pdb=" N TYR C 790 " pdb=" CA TYR C 790 " ideal model delta harmonic sigma weight residual -180.00 -151.27 -28.73 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA GLU C 424 " pdb=" C GLU C 424 " pdb=" N SER C 425 " pdb=" CA SER C 425 " 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 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.426: 2784 0.426 - 0.853: 8 0.853 - 1.279: 0 1.279 - 1.705: 0 1.705 - 2.132: 8 Chirality restraints: 2800 Sorted by residual: 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 2.13 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 1.18 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" C5 CYZ B 902 " pdb=" C4 CYZ B 902 " pdb=" C6 CYZ B 902 " pdb=" C7 CYZ B 902 " both_signs ideal model delta sigma weight residual False 3.31 1.18 2.13 2.00e-01 2.50e+01 1.13e+02 ... (remaining 2797 not shown) Planarity restraints: 3056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 765 " -0.320 9.50e-02 1.11e+02 1.44e-01 1.43e+01 pdb=" NE ARG B 765 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG B 765 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 765 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 765 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 683 " -0.263 9.50e-02 1.11e+02 1.18e-01 9.90e+00 pdb=" NE ARG A 683 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 683 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 683 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 683 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 546 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C GLU D 546 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU D 546 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE D 547 " 0.018 2.00e-02 2.50e+03 ... (remaining 3053 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 524 2.71 - 3.25: 19717 3.25 - 3.80: 29542 3.80 - 4.35: 37258 4.35 - 4.90: 61765 Nonbonded interactions: 148806 Sorted by model distance: nonbonded pdb=" OE1 GLU A 727 " pdb=" OH TYR A 754 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 519 " pdb=" O2 CYZ C 902 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP B 512 " pdb=" NH1 ARG B 765 " model vdw 2.229 3.120 nonbonded pdb=" OE1 GLU C 727 " pdb=" OH TYR C 754 " model vdw 2.237 3.040 nonbonded pdb=" OG SER A 519 " pdb=" O2 CYZ A 902 " model vdw 2.241 3.040 ... (remaining 148801 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.680 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 0.481 18527 Z= 0.804 Angle : 0.855 21.390 25042 Z= 0.419 Chirality : 0.122 2.132 2800 Planarity : 0.008 0.144 3056 Dihedral : 13.555 114.954 6672 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.49 % Allowed : 4.83 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.18 (0.16), residues: 2256 helix: -0.36 (0.13), residues: 1263 sheet: -1.16 (0.45), residues: 128 loop : -1.18 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG B 765 TYR 0.030 0.004 TYR D 472 PHE 0.025 0.002 PHE C 629 TRP 0.027 0.002 TRP C 788 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.01612 (18516) covalent geometry : angle 0.85504 (25020) SS BOND : bond 0.00258 ( 11) SS BOND : angle 0.92080 ( 22) hydrogen bonds : bond 0.12222 ( 1077) hydrogen bonds : angle 5.97598 ( 3087) *********************** 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 526 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.730 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 446 TYR cc_start: 0.8930 (t80) cc_final: 0.8586 (t80) REVERT: A 493 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7322 (mtmm) REVERT: A 541 ASP cc_start: 0.8701 (m-30) cc_final: 0.8418 (m-30) REVERT: A 607 MET cc_start: 0.8912 (mmm) cc_final: 0.8708 (mpp) REVERT: A 641 ASN cc_start: 0.8115 (t0) cc_final: 0.7658 (t0) REVERT: A 730 MET cc_start: 0.9107 (mpp) cc_final: 0.8187 (mpp) REVERT: A 758 THR cc_start: 0.8083 (p) cc_final: 0.7819 (p) REVERT: B 429 MET cc_start: 0.9124 (mtm) cc_final: 0.8803 (mtm) REVERT: B 441 ASP cc_start: 0.8867 (m-30) cc_final: 0.8251 (t0) REVERT: B 562 LEU cc_start: 0.9427 (tt) cc_final: 0.9222 (tp) REVERT: B 692 MET cc_start: 0.9198 (mtp) cc_final: 0.8932 (mtm) REVERT: B 730 MET cc_start: 0.8759 (mpp) cc_final: 0.8452 (mpp) REVERT: B 731 ASN cc_start: 0.8944 (t0) cc_final: 0.8632 (t0) REVERT: B 736 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8770 (mm-40) REVERT: C 493 LYS cc_start: 0.8011 (mttt) cc_final: 0.7735 (mtmm) REVERT: C 525 MET cc_start: 0.8521 (ttm) cc_final: 0.8128 (tpp) REVERT: C 541 ASP cc_start: 0.8240 (m-30) cc_final: 0.7864 (t70) REVERT: C 730 MET cc_start: 0.8954 (mpp) cc_final: 0.8730 (mpp) REVERT: C 731 ASN cc_start: 0.8714 (t0) cc_final: 0.8169 (t0) REVERT: C 754 TYR cc_start: 0.6169 (m-80) cc_final: 0.5806 (m-10) REVERT: C 790 TYR cc_start: 0.8135 (m-80) cc_final: 0.7605 (m-80) REVERT: D 427 TYR cc_start: 0.8565 (m-80) cc_final: 0.7751 (m-80) REVERT: D 489 LEU cc_start: 0.8584 (mt) cc_final: 0.8378 (mt) REVERT: D 518 MET cc_start: 0.8767 (ttm) cc_final: 0.8207 (ttm) REVERT: D 538 SER cc_start: 0.8589 (m) cc_final: 0.8152 (m) REVERT: D 637 SER cc_start: 0.9538 (m) cc_final: 0.9326 (t) REVERT: H 24 MET cc_start: 0.9294 (tpt) cc_final: 0.9063 (tpp) REVERT: F 64 TRP cc_start: 0.8075 (m100) cc_final: 0.7620 (m-10) REVERT: F 185 LEU cc_start: 0.9466 (tp) cc_final: 0.9183 (tp) REVERT: F 206 LYS cc_start: 0.7924 (tttt) cc_final: 0.7712 (ttmt) REVERT: G 58 MET cc_start: 0.8488 (mmm) cc_final: 0.8131 (tpp) REVERT: G 203 ASP cc_start: 0.9135 (t70) cc_final: 0.8874 (t70) REVERT: E 189 ILE cc_start: 0.9265 (mp) cc_final: 0.8998 (mp) REVERT: E 206 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7230 (ttpt) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.1510 time to fit residues: 118.0762 Evaluate side-chains 292 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 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: 10.0000 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 GLN A 736 GLN B 608 GLN B 786 ASN D 786 ASN H 132 HIS H 160 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.104748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080124 restraints weight = 58209.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082253 restraints weight = 24955.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082113 restraints weight = 16792.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082336 restraints weight = 16759.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.082517 restraints weight = 15442.234| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18527 Z= 0.179 Angle : 0.678 10.283 25042 Z= 0.351 Chirality : 0.044 0.219 2800 Planarity : 0.005 0.137 3056 Dihedral : 8.846 96.997 2596 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 2.44 % Allowed : 11.80 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.73 (0.18), residues: 2256 helix: 1.54 (0.15), residues: 1284 sheet: -1.25 (0.40), residues: 171 loop : -0.80 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 682 TYR 0.019 0.002 TYR C 819 PHE 0.016 0.002 PHE A 568 TRP 0.020 0.002 TRP D 789 HIS 0.010 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00407 (18516) covalent geometry : angle 0.67815 (25020) SS BOND : bond 0.00290 ( 11) SS BOND : angle 0.95778 ( 22) hydrogen bonds : bond 0.04272 ( 1077) hydrogen bonds : angle 4.58384 ( 3087) *********************** 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 385 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 338 time to evaluate : 0.569 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 466 ILE cc_start: 0.7238 (mm) cc_final: 0.6828 (mm) REVERT: A 493 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7435 (mtmm) REVERT: A 541 ASP cc_start: 0.8747 (m-30) cc_final: 0.8517 (m-30) REVERT: A 641 ASN cc_start: 0.8266 (t0) cc_final: 0.7888 (t0) REVERT: A 819 TYR cc_start: 0.8975 (m-80) cc_final: 0.8668 (m-80) REVERT: B 441 ASP cc_start: 0.8700 (m-30) cc_final: 0.8268 (t0) REVERT: B 525 MET cc_start: 0.8786 (tmm) cc_final: 0.8477 (tmm) REVERT: B 692 MET cc_start: 0.9270 (mtp) cc_final: 0.8690 (mtp) REVERT: B 736 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8617 (mm-40) REVERT: B 744 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8873 (ttmm) REVERT: C 525 MET cc_start: 0.8608 (ttm) cc_final: 0.8124 (tpt) REVERT: C 730 MET cc_start: 0.9315 (mpp) cc_final: 0.9084 (mpp) REVERT: D 427 TYR cc_start: 0.8636 (m-80) cc_final: 0.8266 (m-80) REVERT: D 518 MET cc_start: 0.8930 (ttm) cc_final: 0.8577 (ttm) REVERT: D 525 MET cc_start: 0.9048 (ppp) cc_final: 0.8519 (ppp) REVERT: D 538 SER cc_start: 0.8630 (m) cc_final: 0.8257 (m) REVERT: D 541 ASP cc_start: 0.8496 (m-30) cc_final: 0.8292 (m-30) REVERT: D 637 SER cc_start: 0.9584 (m) cc_final: 0.9313 (t) REVERT: D 769 ASN cc_start: 0.8478 (m-40) cc_final: 0.8135 (m110) REVERT: H 24 MET cc_start: 0.9468 (tpt) cc_final: 0.9068 (tpp) REVERT: H 81 ASP cc_start: 0.8253 (t0) cc_final: 0.8022 (t0) REVERT: H 117 MET cc_start: 0.9186 (mmm) cc_final: 0.8694 (mpp) REVERT: H 156 TYR cc_start: 0.9200 (t80) cc_final: 0.8977 (t80) REVERT: H 207 GLN cc_start: 0.8071 (tt0) cc_final: 0.7198 (tp40) REVERT: F 185 LEU cc_start: 0.9448 (tp) cc_final: 0.9182 (tp) REVERT: F 206 LYS cc_start: 0.8042 (tttt) cc_final: 0.7745 (ttmt) REVERT: E 95 GLU cc_start: 0.8589 (pm20) cc_final: 0.8086 (pp20) REVERT: E 99 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7025 (mmm160) REVERT: E 180 PHE cc_start: 0.8870 (t80) cc_final: 0.8643 (t80) REVERT: E 206 LYS cc_start: 0.7453 (ttpt) cc_final: 0.7067 (ttpt) REVERT: E 207 GLN cc_start: 0.7457 (mp10) cc_final: 0.7169 (mm110) outliers start: 47 outliers final: 24 residues processed: 362 average time/residue: 0.1163 time to fit residues: 65.0547 Evaluate side-chains 284 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 744 LYS Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 680 PHE Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 224 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 chunk 177 optimal weight: 0.0170 chunk 89 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN B 786 ASN D 736 GLN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.075086 restraints weight = 56511.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077277 restraints weight = 29199.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078685 restraints weight = 19669.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079483 restraints weight = 15559.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.079749 restraints weight = 13644.294| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18527 Z= 0.123 Angle : 0.612 8.912 25042 Z= 0.312 Chirality : 0.042 0.194 2800 Planarity : 0.004 0.073 3056 Dihedral : 8.113 92.627 2596 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 2.44 % Allowed : 13.83 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.28 (0.18), residues: 2256 helix: 2.10 (0.15), residues: 1271 sheet: -1.44 (0.38), residues: 176 loop : -0.62 (0.23), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 37 TYR 0.027 0.001 TYR C 819 PHE 0.018 0.001 PHE E 180 TRP 0.013 0.001 TRP C 788 HIS 0.007 0.001 HIS G 132 Details of bonding type rmsd covalent geometry : bond 0.00269 (18516) covalent geometry : angle 0.61154 (25020) SS BOND : bond 0.00300 ( 11) SS BOND : angle 1.03721 ( 22) hydrogen bonds : bond 0.03712 ( 1077) hydrogen bonds : angle 4.15847 ( 3087) *********************** 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 362 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 315 time to evaluate : 0.790 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 472 TYR cc_start: 0.8311 (m-80) cc_final: 0.8105 (m-10) REVERT: A 493 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7416 (mtmm) REVERT: A 541 ASP cc_start: 0.8750 (m-30) cc_final: 0.8516 (m-30) REVERT: A 641 ASN cc_start: 0.8384 (t0) cc_final: 0.7985 (t0) REVERT: A 819 TYR cc_start: 0.8985 (m-80) cc_final: 0.8691 (m-80) REVERT: B 423 MET cc_start: 0.8520 (pmm) cc_final: 0.7564 (tpt) REVERT: B 441 ASP cc_start: 0.8614 (m-30) cc_final: 0.8334 (t0) REVERT: B 485 MET cc_start: 0.7265 (mtm) cc_final: 0.6431 (mtt) REVERT: B 525 MET cc_start: 0.8770 (tmm) cc_final: 0.8517 (tmm) REVERT: B 692 MET cc_start: 0.9256 (mtp) cc_final: 0.8559 (mtp) REVERT: B 736 GLN cc_start: 0.9325 (mm-40) cc_final: 0.8577 (mm-40) REVERT: B 774 LYS cc_start: 0.9187 (pttp) cc_final: 0.8943 (ptmm) REVERT: B 786 ASN cc_start: 0.9205 (m110) cc_final: 0.8826 (p0) REVERT: C 525 MET cc_start: 0.8596 (ttm) cc_final: 0.8038 (tpp) REVERT: C 726 LEU cc_start: 0.9542 (tp) cc_final: 0.9326 (tp) REVERT: C 730 MET cc_start: 0.9317 (mpp) cc_final: 0.9064 (mpp) REVERT: C 754 TYR cc_start: 0.6318 (m-80) cc_final: 0.6033 (m-10) REVERT: D 427 TYR cc_start: 0.8530 (m-80) cc_final: 0.8000 (m-80) REVERT: D 518 MET cc_start: 0.8982 (ttm) cc_final: 0.8504 (ttm) REVERT: D 525 MET cc_start: 0.9111 (ppp) cc_final: 0.8367 (ppp) REVERT: D 538 SER cc_start: 0.8580 (m) cc_final: 0.8009 (m) REVERT: D 541 ASP cc_start: 0.8436 (m-30) cc_final: 0.8166 (m-30) REVERT: D 637 SER cc_start: 0.9625 (m) cc_final: 0.9333 (t) REVERT: D 692 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.9168 (mpp) REVERT: D 769 ASN cc_start: 0.8546 (m-40) cc_final: 0.8231 (m110) REVERT: H 24 MET cc_start: 0.9486 (tpt) cc_final: 0.9060 (tpp) REVERT: H 59 THR cc_start: 0.7402 (OUTLIER) cc_final: 0.7091 (m) REVERT: H 81 ASP cc_start: 0.8154 (t0) cc_final: 0.7846 (t0) REVERT: H 174 TYR cc_start: 0.8061 (p90) cc_final: 0.7454 (p90) REVERT: H 207 GLN cc_start: 0.8007 (tt0) cc_final: 0.7166 (tp40) REVERT: F 120 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8014 (tp) REVERT: F 185 LEU cc_start: 0.9462 (tp) cc_final: 0.9206 (tp) REVERT: F 206 LYS cc_start: 0.7985 (tttt) cc_final: 0.7640 (ttmt) REVERT: E 95 GLU cc_start: 0.8477 (pm20) cc_final: 0.7969 (pp20) REVERT: B 901 GLU cc_start: 0.6562 (tp30) cc_final: 0.5668 (tp30) outliers start: 47 outliers final: 22 residues processed: 344 average time/residue: 0.1248 time to fit residues: 67.7257 Evaluate side-chains 287 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 262 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 680 PHE Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 195 optimal weight: 0.9980 chunk 211 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 786 ASN H 160 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.100334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072779 restraints weight = 58638.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.074678 restraints weight = 32527.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.075459 restraints weight = 20144.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.075796 restraints weight = 17462.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.075898 restraints weight = 16392.468| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18527 Z= 0.157 Angle : 0.609 11.964 25042 Z= 0.312 Chirality : 0.042 0.218 2800 Planarity : 0.004 0.052 3056 Dihedral : 7.534 88.294 2596 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 3.33 % Allowed : 15.02 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.33 (0.18), residues: 2256 helix: 2.10 (0.15), residues: 1289 sheet: -1.43 (0.39), residues: 157 loop : -0.62 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.030 0.001 TYR C 819 PHE 0.014 0.001 PHE H 201 TRP 0.020 0.001 TRP A 482 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00354 (18516) covalent geometry : angle 0.60816 (25020) SS BOND : bond 0.00212 ( 11) SS BOND : angle 0.98849 ( 22) hydrogen bonds : bond 0.03743 ( 1077) hydrogen bonds : angle 4.19822 ( 3087) *********************** 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 347 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 0.714 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 493 LYS cc_start: 0.7791 (mtmm) cc_final: 0.7417 (mtmm) REVERT: A 641 ASN cc_start: 0.8497 (t0) cc_final: 0.8035 (t0) REVERT: A 743 MET cc_start: 0.8372 (ppp) cc_final: 0.7953 (ppp) REVERT: A 819 TYR cc_start: 0.8963 (m-80) cc_final: 0.8692 (m-80) REVERT: B 429 MET cc_start: 0.9022 (mtp) cc_final: 0.8794 (mpp) REVERT: B 485 MET cc_start: 0.7286 (mtm) cc_final: 0.7008 (mtt) REVERT: B 520 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8833 (pp) REVERT: B 525 MET cc_start: 0.8781 (tmm) cc_final: 0.8509 (tmm) REVERT: B 692 MET cc_start: 0.9365 (mtp) cc_final: 0.8798 (mtt) REVERT: B 736 GLN cc_start: 0.9295 (mm-40) cc_final: 0.9052 (mm-40) REVERT: B 785 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9045 (mtmt) REVERT: C 423 MET cc_start: 0.8653 (mmm) cc_final: 0.8372 (tpp) REVERT: C 457 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6335 (m-70) REVERT: C 525 MET cc_start: 0.8536 (ttm) cc_final: 0.7915 (tpp) REVERT: C 692 MET cc_start: 0.9439 (ptt) cc_final: 0.9104 (ppp) REVERT: C 726 LEU cc_start: 0.9552 (tp) cc_final: 0.8985 (tp) REVERT: C 730 MET cc_start: 0.9323 (mpp) cc_final: 0.9001 (mpp) REVERT: C 754 TYR cc_start: 0.6415 (m-80) cc_final: 0.6120 (m-10) REVERT: D 427 TYR cc_start: 0.8569 (m-80) cc_final: 0.8136 (m-80) REVERT: D 518 MET cc_start: 0.9126 (ttm) cc_final: 0.8729 (ttm) REVERT: D 525 MET cc_start: 0.9114 (ppp) cc_final: 0.8452 (ppp) REVERT: D 769 ASN cc_start: 0.8603 (m-40) cc_final: 0.8234 (m110) REVERT: H 24 MET cc_start: 0.9516 (tpt) cc_final: 0.9316 (tpp) REVERT: H 59 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7188 (m) REVERT: H 81 ASP cc_start: 0.8404 (t0) cc_final: 0.8074 (t0) REVERT: H 174 TYR cc_start: 0.8196 (p90) cc_final: 0.7583 (p90) REVERT: H 207 GLN cc_start: 0.8110 (tt0) cc_final: 0.7178 (tp40) REVERT: F 9 GLN cc_start: 0.8336 (mp10) cc_final: 0.8093 (mp10) REVERT: F 185 LEU cc_start: 0.9465 (tp) cc_final: 0.9228 (tp) REVERT: F 206 LYS cc_start: 0.8073 (tttt) cc_final: 0.7763 (ttmt) REVERT: G 191 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8644 (tp30) REVERT: E 58 MET cc_start: 0.8442 (tpp) cc_final: 0.8096 (tmm) REVERT: E 70 GLU cc_start: 0.8405 (mp0) cc_final: 0.7867 (pp20) REVERT: E 95 GLU cc_start: 0.8633 (pm20) cc_final: 0.8132 (pp20) REVERT: E 99 ARG cc_start: 0.9009 (tpp80) cc_final: 0.8769 (tpp80) REVERT: E 110 LEU cc_start: 0.9419 (tp) cc_final: 0.9146 (tp) outliers start: 64 outliers final: 40 residues processed: 320 average time/residue: 0.1256 time to fit residues: 63.0162 Evaluate side-chains 303 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 260 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 94 optimal weight: 4.9990 chunk 199 optimal weight: 0.0970 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN B 786 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.099747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.071888 restraints weight = 58923.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073868 restraints weight = 32074.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074612 restraints weight = 20106.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.074879 restraints weight = 17462.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074994 restraints weight = 16645.938| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18527 Z= 0.175 Angle : 0.624 16.092 25042 Z= 0.315 Chirality : 0.042 0.238 2800 Planarity : 0.004 0.050 3056 Dihedral : 6.968 85.149 2596 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.77 % Favored : 96.19 % Rotamer: Outliers : 3.69 % Allowed : 16.63 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.30 (0.18), residues: 2256 helix: 2.12 (0.15), residues: 1288 sheet: -1.65 (0.37), residues: 178 loop : -0.62 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 204 TYR 0.026 0.001 TYR A 472 PHE 0.015 0.001 PHE H 201 TRP 0.025 0.001 TRP A 482 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00397 (18516) covalent geometry : angle 0.62386 (25020) SS BOND : bond 0.00199 ( 11) SS BOND : angle 0.87573 ( 22) hydrogen bonds : bond 0.03823 ( 1077) hydrogen bonds : angle 4.23054 ( 3087) *********************** 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 339 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8324 (tp30) REVERT: A 493 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7379 (mtmm) REVERT: A 641 ASN cc_start: 0.8679 (t0) cc_final: 0.8193 (t0) REVERT: A 743 MET cc_start: 0.8354 (ppp) cc_final: 0.7962 (ppp) REVERT: A 819 TYR cc_start: 0.8981 (m-80) cc_final: 0.8748 (m-80) REVERT: B 423 MET cc_start: 0.8698 (pmm) cc_final: 0.7471 (tpt) REVERT: B 485 MET cc_start: 0.7265 (mtm) cc_final: 0.6997 (mtt) REVERT: B 520 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8896 (pp) REVERT: B 525 MET cc_start: 0.8880 (tmm) cc_final: 0.8628 (tmm) REVERT: B 692 MET cc_start: 0.9405 (mtp) cc_final: 0.8711 (mtp) REVERT: B 730 MET cc_start: 0.9305 (mpp) cc_final: 0.8924 (pmm) REVERT: B 736 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8830 (mm-40) REVERT: B 786 ASN cc_start: 0.9338 (m110) cc_final: 0.8950 (p0) REVERT: C 457 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6604 (m-70) REVERT: C 525 MET cc_start: 0.8584 (ttm) cc_final: 0.7855 (tpp) REVERT: C 692 MET cc_start: 0.9430 (ptt) cc_final: 0.9130 (ppp) REVERT: C 726 LEU cc_start: 0.9449 (tp) cc_final: 0.9152 (tp) REVERT: C 754 TYR cc_start: 0.6397 (m-80) cc_final: 0.6054 (m-10) REVERT: D 427 TYR cc_start: 0.8595 (m-80) cc_final: 0.8309 (m-80) REVERT: D 518 MET cc_start: 0.9172 (ttm) cc_final: 0.8803 (ttm) REVERT: D 525 MET cc_start: 0.9098 (ppp) cc_final: 0.8723 (ppp) REVERT: D 607 MET cc_start: 0.8636 (mmm) cc_final: 0.8344 (mmm) REVERT: H 24 MET cc_start: 0.9556 (tpt) cc_final: 0.9214 (tpp) REVERT: H 59 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7377 (m) REVERT: H 81 ASP cc_start: 0.8530 (t0) cc_final: 0.8172 (t0) REVERT: H 174 TYR cc_start: 0.8278 (p90) cc_final: 0.7642 (p90) REVERT: H 207 GLN cc_start: 0.8200 (tt0) cc_final: 0.7276 (tp40) REVERT: F 99 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8645 (ttm-80) REVERT: F 120 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8094 (tp) REVERT: F 185 LEU cc_start: 0.9479 (tp) cc_final: 0.9248 (tp) REVERT: G 129 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8584 (tppt) REVERT: E 32 TYR cc_start: 0.8161 (m-80) cc_final: 0.7565 (m-80) REVERT: E 58 MET cc_start: 0.8421 (tpp) cc_final: 0.8026 (tmm) REVERT: E 70 GLU cc_start: 0.8435 (mp0) cc_final: 0.7947 (pp20) REVERT: E 95 GLU cc_start: 0.8728 (pm20) cc_final: 0.8260 (pp20) REVERT: E 99 ARG cc_start: 0.9080 (tpp80) cc_final: 0.8866 (tpp80) REVERT: E 110 LEU cc_start: 0.9436 (tp) cc_final: 0.9155 (tp) REVERT: E 180 PHE cc_start: 0.9146 (t80) cc_final: 0.8940 (t80) REVERT: B 901 GLU cc_start: 0.6759 (tp30) cc_final: 0.5559 (tp30) outliers start: 71 outliers final: 47 residues processed: 312 average time/residue: 0.1175 time to fit residues: 58.1590 Evaluate side-chains 298 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 246 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 645 PHE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 790 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 772 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 82 HIS Chi-restraints excluded: chain G residue 97 PHE Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 109 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 184 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN B 457 HIS D 736 GLN H 160 ASN G 160 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.074568 restraints weight = 57012.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.076429 restraints weight = 32208.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.076636 restraints weight = 20719.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076812 restraints weight = 21024.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.076952 restraints weight = 19865.318| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18527 Z= 0.115 Angle : 0.596 14.700 25042 Z= 0.296 Chirality : 0.042 0.244 2800 Planarity : 0.004 0.052 3056 Dihedral : 6.165 81.602 2596 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 2.96 % Allowed : 18.19 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.50 (0.19), residues: 2256 helix: 2.32 (0.15), residues: 1276 sheet: -1.38 (0.40), residues: 156 loop : -0.65 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.024 0.001 TYR A 695 PHE 0.017 0.001 PHE C 629 TRP 0.023 0.001 TRP A 482 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00251 (18516) covalent geometry : angle 0.59570 (25020) SS BOND : bond 0.00183 ( 11) SS BOND : angle 0.81358 ( 22) hydrogen bonds : bond 0.03520 ( 1077) hydrogen bonds : angle 4.02718 ( 3087) *********************** 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 348 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 291 time to evaluate : 0.777 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 453 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8291 (tp30) REVERT: A 493 LYS cc_start: 0.7777 (mtmm) cc_final: 0.7372 (mtmm) REVERT: A 641 ASN cc_start: 0.8564 (t0) cc_final: 0.8139 (t0) REVERT: A 661 LEU cc_start: 0.8487 (tp) cc_final: 0.8070 (pp) REVERT: A 743 MET cc_start: 0.8380 (ppp) cc_final: 0.8032 (ppp) REVERT: A 819 TYR cc_start: 0.8970 (m-80) cc_final: 0.8686 (m-80) REVERT: B 423 MET cc_start: 0.8463 (pmm) cc_final: 0.7468 (tpt) REVERT: B 457 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.6716 (m-70) REVERT: B 485 MET cc_start: 0.7056 (mtm) cc_final: 0.6825 (mtt) REVERT: B 520 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 525 MET cc_start: 0.8731 (tmm) cc_final: 0.8464 (tmm) REVERT: B 692 MET cc_start: 0.9325 (mtp) cc_final: 0.8764 (mtp) REVERT: B 736 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8752 (mm-40) REVERT: B 785 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9110 (mmmt) REVERT: B 786 ASN cc_start: 0.9255 (m110) cc_final: 0.8811 (p0) REVERT: C 525 MET cc_start: 0.8471 (ttm) cc_final: 0.8173 (tpp) REVERT: C 692 MET cc_start: 0.9364 (ptt) cc_final: 0.9084 (ppp) REVERT: D 427 TYR cc_start: 0.8494 (m-80) cc_final: 0.8149 (m-80) REVERT: D 443 TYR cc_start: 0.8004 (m-80) cc_final: 0.7530 (m-10) REVERT: D 518 MET cc_start: 0.9072 (ttm) cc_final: 0.8732 (ttm) REVERT: D 525 MET cc_start: 0.9054 (ppp) cc_final: 0.8730 (ppp) REVERT: H 24 MET cc_start: 0.9448 (tpt) cc_final: 0.9057 (tpp) REVERT: H 59 THR cc_start: 0.7445 (OUTLIER) cc_final: 0.7046 (m) REVERT: H 81 ASP cc_start: 0.8359 (t0) cc_final: 0.7980 (t0) REVERT: H 174 TYR cc_start: 0.8090 (p90) cc_final: 0.7475 (p90) REVERT: H 207 GLN cc_start: 0.8183 (tt0) cc_final: 0.7208 (tp40) REVERT: F 99 ARG cc_start: 0.8710 (tpp80) cc_final: 0.8469 (ttm-80) REVERT: F 106 ILE cc_start: 0.8741 (tt) cc_final: 0.8482 (tp) REVERT: F 120 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7988 (tp) REVERT: G 129 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8593 (mmmt) REVERT: E 10 MET cc_start: 0.7653 (mpp) cc_final: 0.6990 (mtp) REVERT: E 95 GLU cc_start: 0.8610 (pm20) cc_final: 0.8278 (pp20) REVERT: E 110 LEU cc_start: 0.9431 (tp) cc_final: 0.9152 (tp) REVERT: E 180 PHE cc_start: 0.9025 (t80) cc_final: 0.8794 (t80) outliers start: 57 outliers final: 41 residues processed: 324 average time/residue: 0.1289 time to fit residues: 65.1232 Evaluate side-chains 304 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 429 MET Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 78 LYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 222 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 ASN A 609 GLN F 132 HIS G 160 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.102133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.076646 restraints weight = 56826.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077459 restraints weight = 31913.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.077579 restraints weight = 24645.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.077843 restraints weight = 23035.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.077971 restraints weight = 21691.255| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18527 Z= 0.121 Angle : 0.605 14.076 25042 Z= 0.298 Chirality : 0.041 0.220 2800 Planarity : 0.004 0.052 3056 Dihedral : 5.656 79.539 2596 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 3.07 % Allowed : 19.02 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.44 (0.19), residues: 2256 helix: 2.27 (0.15), residues: 1283 sheet: -1.63 (0.40), residues: 153 loop : -0.66 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.022 0.001 TYR C 819 PHE 0.015 0.001 PHE C 629 TRP 0.018 0.001 TRP A 482 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00269 (18516) covalent geometry : angle 0.60462 (25020) SS BOND : bond 0.00164 ( 11) SS BOND : angle 0.78428 ( 22) hydrogen bonds : bond 0.03501 ( 1077) hydrogen bonds : angle 4.02400 ( 3087) *********************** 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 330 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 0.763 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 453 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8227 (tp30) REVERT: A 493 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7459 (mtmm) REVERT: A 641 ASN cc_start: 0.8480 (t0) cc_final: 0.8113 (t0) REVERT: A 661 LEU cc_start: 0.8563 (tp) cc_final: 0.8203 (pp) REVERT: A 743 MET cc_start: 0.8349 (ppp) cc_final: 0.8065 (ppp) REVERT: A 819 TYR cc_start: 0.8929 (m-80) cc_final: 0.8627 (m-80) REVERT: B 423 MET cc_start: 0.8280 (pmm) cc_final: 0.7445 (tpt) REVERT: B 429 MET cc_start: 0.8251 (mpp) cc_final: 0.7985 (mpp) REVERT: B 485 MET cc_start: 0.7065 (mtm) cc_final: 0.6738 (mtt) REVERT: B 520 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8857 (pp) REVERT: B 692 MET cc_start: 0.9232 (mtp) cc_final: 0.8680 (mtp) REVERT: B 736 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8759 (mm-40) REVERT: B 785 LYS cc_start: 0.9525 (mmmt) cc_final: 0.9173 (mttp) REVERT: B 786 ASN cc_start: 0.9189 (m110) cc_final: 0.8722 (p0) REVERT: C 457 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.6180 (m-70) REVERT: C 525 MET cc_start: 0.8454 (ttm) cc_final: 0.8126 (tpp) REVERT: D 427 TYR cc_start: 0.8437 (m-80) cc_final: 0.8098 (m-80) REVERT: D 443 TYR cc_start: 0.7765 (m-80) cc_final: 0.7367 (m-10) REVERT: D 518 MET cc_start: 0.9046 (ttm) cc_final: 0.8727 (ttm) REVERT: D 525 MET cc_start: 0.8989 (ppp) cc_final: 0.8743 (ppp) REVERT: H 59 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7240 (m) REVERT: H 81 ASP cc_start: 0.8280 (t0) cc_final: 0.7927 (t0) REVERT: H 174 TYR cc_start: 0.8032 (p90) cc_final: 0.7447 (p90) REVERT: H 207 GLN cc_start: 0.8128 (tt0) cc_final: 0.7147 (tp40) REVERT: F 99 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8375 (ttm-80) REVERT: F 106 ILE cc_start: 0.8854 (tt) cc_final: 0.8585 (tp) REVERT: F 120 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (tp) REVERT: G 191 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8446 (mm-30) REVERT: E 95 GLU cc_start: 0.8469 (pm20) cc_final: 0.8159 (pp20) REVERT: E 110 LEU cc_start: 0.9403 (tp) cc_final: 0.9118 (tp) REVERT: E 180 PHE cc_start: 0.8866 (t80) cc_final: 0.8622 (t80) REVERT: B 901 GLU cc_start: 0.6733 (mm-30) cc_final: 0.5967 (mm-30) outliers start: 59 outliers final: 45 residues processed: 306 average time/residue: 0.1223 time to fit residues: 59.9598 Evaluate side-chains 306 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 160 ASN Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 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 433 ASN H 160 ASN F 132 HIS F 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.101943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075361 restraints weight = 58444.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076586 restraints weight = 29036.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.076744 restraints weight = 20348.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077216 restraints weight = 20030.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077546 restraints weight = 18951.210| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18527 Z= 0.122 Angle : 0.619 14.616 25042 Z= 0.302 Chirality : 0.041 0.294 2800 Planarity : 0.004 0.074 3056 Dihedral : 5.453 78.497 2596 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 3.33 % Allowed : 19.54 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.50 (0.19), residues: 2256 helix: 2.33 (0.15), residues: 1275 sheet: -1.87 (0.38), residues: 166 loop : -0.53 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 99 TYR 0.019 0.001 TYR C 819 PHE 0.014 0.001 PHE C 629 TRP 0.014 0.001 TRP A 482 HIS 0.006 0.001 HIS F 132 Details of bonding type rmsd covalent geometry : bond 0.00272 (18516) covalent geometry : angle 0.61937 (25020) SS BOND : bond 0.00175 ( 11) SS BOND : angle 0.74324 ( 22) hydrogen bonds : bond 0.03491 ( 1077) hydrogen bonds : angle 4.00824 ( 3087) *********************** 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 334 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 270 time to evaluate : 0.627 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 446 TYR cc_start: 0.8568 (t80) cc_final: 0.8145 (t80) REVERT: A 453 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8369 (tp30) REVERT: A 493 LYS cc_start: 0.7735 (mtmm) cc_final: 0.7332 (mtmm) REVERT: A 518 MET cc_start: 0.8067 (mmm) cc_final: 0.7703 (mmm) REVERT: A 641 ASN cc_start: 0.8696 (t0) cc_final: 0.8243 (t0) REVERT: A 661 LEU cc_start: 0.8636 (tp) cc_final: 0.8294 (pp) REVERT: A 743 MET cc_start: 0.8336 (ppp) cc_final: 0.8044 (ppp) REVERT: A 819 TYR cc_start: 0.8998 (m-80) cc_final: 0.8751 (m-80) REVERT: B 423 MET cc_start: 0.8538 (pmm) cc_final: 0.7585 (tpt) REVERT: B 429 MET cc_start: 0.8292 (mpp) cc_final: 0.8054 (mpp) REVERT: B 485 MET cc_start: 0.7091 (mtm) cc_final: 0.6775 (mtt) REVERT: B 520 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 525 MET cc_start: 0.8687 (tmm) cc_final: 0.8486 (tmm) REVERT: B 692 MET cc_start: 0.9365 (mtp) cc_final: 0.8688 (mtp) REVERT: B 736 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8792 (mm-40) REVERT: B 785 LYS cc_start: 0.9541 (mmmt) cc_final: 0.9234 (mmmt) REVERT: B 786 ASN cc_start: 0.9303 (m110) cc_final: 0.8864 (p0) REVERT: C 457 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6580 (m-70) REVERT: C 525 MET cc_start: 0.8488 (ttm) cc_final: 0.7915 (tpp) REVERT: C 696 MET cc_start: 0.7823 (mmm) cc_final: 0.7474 (mmm) REVERT: D 427 TYR cc_start: 0.8447 (m-80) cc_final: 0.8080 (m-80) REVERT: D 443 TYR cc_start: 0.7948 (m-80) cc_final: 0.7502 (m-10) REVERT: D 518 MET cc_start: 0.9186 (ttm) cc_final: 0.8767 (ttm) REVERT: D 525 MET cc_start: 0.9060 (ppp) cc_final: 0.8716 (ppp) REVERT: D 735 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8852 (pp20) REVERT: H 81 ASP cc_start: 0.8441 (t0) cc_final: 0.8059 (t0) REVERT: H 174 TYR cc_start: 0.8241 (p90) cc_final: 0.7553 (p90) REVERT: H 207 GLN cc_start: 0.8197 (tt0) cc_final: 0.7209 (tp40) REVERT: F 99 ARG cc_start: 0.8783 (tpp80) cc_final: 0.8508 (ttm-80) REVERT: F 102 ARG cc_start: 0.9345 (tpt90) cc_final: 0.8766 (tpt90) REVERT: F 106 ILE cc_start: 0.8668 (tt) cc_final: 0.8424 (tp) REVERT: F 120 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8025 (tp) REVERT: G 191 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 32 TYR cc_start: 0.8010 (m-80) cc_final: 0.7464 (m-10) REVERT: E 95 GLU cc_start: 0.8683 (pm20) cc_final: 0.8314 (pp20) REVERT: E 110 LEU cc_start: 0.9451 (tp) cc_final: 0.9183 (tp) REVERT: E 180 PHE cc_start: 0.9049 (t80) cc_final: 0.8796 (t80) outliers start: 64 outliers final: 52 residues processed: 308 average time/residue: 0.1111 time to fit residues: 54.6577 Evaluate side-chains 318 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 263 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 418 VAL Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 745 VAL Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 216 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.102561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.075642 restraints weight = 57200.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077763 restraints weight = 30354.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078149 restraints weight = 18326.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078368 restraints weight = 17419.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078466 restraints weight = 17004.074| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18527 Z= 0.123 Angle : 0.622 15.159 25042 Z= 0.301 Chirality : 0.041 0.258 2800 Planarity : 0.004 0.051 3056 Dihedral : 5.263 78.583 2596 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 2.96 % Allowed : 19.65 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.53 (0.19), residues: 2256 helix: 2.35 (0.15), residues: 1275 sheet: -1.66 (0.41), residues: 146 loop : -0.60 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 204 TYR 0.019 0.001 TYR B 638 PHE 0.012 0.001 PHE C 629 TRP 0.012 0.001 TRP A 482 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00274 (18516) covalent geometry : angle 0.62154 (25020) SS BOND : bond 0.00158 ( 11) SS BOND : angle 0.71940 ( 22) hydrogen bonds : bond 0.03458 ( 1077) hydrogen bonds : angle 3.99386 ( 3087) *********************** 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 330 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 273 time to evaluate : 0.705 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 453 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8566 (tp30) REVERT: A 493 LYS cc_start: 0.7763 (mtmm) cc_final: 0.7356 (mtmm) REVERT: A 518 MET cc_start: 0.8002 (mmm) cc_final: 0.7695 (mmm) REVERT: A 641 ASN cc_start: 0.8688 (t0) cc_final: 0.8251 (t0) REVERT: A 661 LEU cc_start: 0.8635 (tp) cc_final: 0.8296 (pp) REVERT: A 743 MET cc_start: 0.8309 (ppp) cc_final: 0.8055 (ppp) REVERT: A 819 TYR cc_start: 0.8979 (m-80) cc_final: 0.8712 (m-80) REVERT: B 423 MET cc_start: 0.8515 (pmm) cc_final: 0.7577 (tpt) REVERT: B 429 MET cc_start: 0.8310 (mpp) cc_final: 0.8102 (mpp) REVERT: B 485 MET cc_start: 0.7095 (mtm) cc_final: 0.6782 (mtt) REVERT: B 520 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8744 (pp) REVERT: B 525 MET cc_start: 0.8712 (tmm) cc_final: 0.8488 (tmm) REVERT: B 692 MET cc_start: 0.9346 (mtp) cc_final: 0.8709 (mtp) REVERT: B 785 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9175 (mtmt) REVERT: B 786 ASN cc_start: 0.9292 (m110) cc_final: 0.8848 (p0) REVERT: C 457 HIS cc_start: 0.7079 (OUTLIER) cc_final: 0.6547 (m-70) REVERT: C 525 MET cc_start: 0.8419 (ttm) cc_final: 0.7869 (tpp) REVERT: C 696 MET cc_start: 0.7807 (mmm) cc_final: 0.7521 (mmm) REVERT: D 427 TYR cc_start: 0.8435 (m-80) cc_final: 0.8172 (m-10) REVERT: D 518 MET cc_start: 0.9212 (ttm) cc_final: 0.8809 (ttm) REVERT: D 525 MET cc_start: 0.9061 (ppp) cc_final: 0.8714 (ppp) REVERT: D 696 MET cc_start: 0.9222 (tpp) cc_final: 0.8986 (tpp) REVERT: D 735 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8852 (pp20) REVERT: H 24 MET cc_start: 0.9285 (tpp) cc_final: 0.9020 (tpp) REVERT: H 81 ASP cc_start: 0.8404 (t0) cc_final: 0.8024 (t0) REVERT: H 174 TYR cc_start: 0.8246 (p90) cc_final: 0.7581 (p90) REVERT: H 207 GLN cc_start: 0.8178 (tt0) cc_final: 0.7185 (tp40) REVERT: F 65 ARG cc_start: 0.7861 (ptm-80) cc_final: 0.7631 (mtm110) REVERT: F 99 ARG cc_start: 0.8748 (tpp80) cc_final: 0.8487 (ttm-80) REVERT: F 102 ARG cc_start: 0.9339 (tpt90) cc_final: 0.8767 (tpt90) REVERT: F 106 ILE cc_start: 0.8689 (tt) cc_final: 0.8455 (tp) REVERT: F 120 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7983 (tp) REVERT: G 191 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8552 (mm-30) REVERT: E 32 TYR cc_start: 0.8005 (m-80) cc_final: 0.7477 (m-10) REVERT: E 70 GLU cc_start: 0.8539 (mp0) cc_final: 0.8251 (pp20) REVERT: E 95 GLU cc_start: 0.8547 (pm20) cc_final: 0.8225 (pp20) REVERT: E 110 LEU cc_start: 0.9465 (tp) cc_final: 0.9200 (tp) REVERT: E 180 PHE cc_start: 0.9014 (t80) cc_final: 0.8768 (t80) REVERT: B 901 GLU cc_start: 0.6757 (mm-30) cc_final: 0.5902 (mm-30) outliers start: 57 outliers final: 47 residues processed: 305 average time/residue: 0.1143 time to fit residues: 55.5233 Evaluate side-chains 312 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 201 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 216 optimal weight: 0.4980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 160 ASN ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.100308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.074674 restraints weight = 57556.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.075801 restraints weight = 32584.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.075986 restraints weight = 23398.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076192 restraints weight = 21456.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.076336 restraints weight = 20425.105| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18527 Z= 0.175 Angle : 0.671 15.531 25042 Z= 0.330 Chirality : 0.042 0.270 2800 Planarity : 0.004 0.050 3056 Dihedral : 5.345 81.763 2596 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 2.91 % Allowed : 20.43 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.36 (0.19), residues: 2256 helix: 2.21 (0.15), residues: 1285 sheet: -1.95 (0.39), residues: 156 loop : -0.64 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 204 TYR 0.022 0.001 TYR C 819 PHE 0.014 0.001 PHE H 201 TRP 0.030 0.001 TRP C 788 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00397 (18516) covalent geometry : angle 0.66992 (25020) SS BOND : bond 0.00515 ( 11) SS BOND : angle 1.43455 ( 22) hydrogen bonds : bond 0.03776 ( 1077) hydrogen bonds : angle 4.17326 ( 3087) ********************** 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 317 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7902 (mmm) cc_final: 0.7526 (mmm) REVERT: A 446 TYR cc_start: 0.8566 (t80) cc_final: 0.8277 (t80) REVERT: A 453 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8484 (tp30) REVERT: A 493 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7447 (mtmm) REVERT: A 518 MET cc_start: 0.7900 (mmm) cc_final: 0.7644 (mmm) REVERT: A 525 MET cc_start: 0.7884 (ttp) cc_final: 0.7214 (tpp) REVERT: A 641 ASN cc_start: 0.8642 (t0) cc_final: 0.8219 (t0) REVERT: A 819 TYR cc_start: 0.8946 (m-80) cc_final: 0.8668 (m-80) REVERT: B 423 MET cc_start: 0.8345 (pmm) cc_final: 0.7480 (tpt) REVERT: B 429 MET cc_start: 0.8276 (mpp) cc_final: 0.8045 (mpp) REVERT: B 485 MET cc_start: 0.7268 (mtm) cc_final: 0.6932 (mtt) REVERT: B 520 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8823 (pp) REVERT: B 525 MET cc_start: 0.8710 (tmm) cc_final: 0.8487 (tmm) REVERT: B 692 MET cc_start: 0.9246 (mtp) cc_final: 0.8775 (mtp) REVERT: B 785 LYS cc_start: 0.9519 (mmmt) cc_final: 0.9161 (mmmt) REVERT: B 786 ASN cc_start: 0.9203 (m110) cc_final: 0.8794 (p0) REVERT: C 457 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.6239 (m-70) REVERT: C 525 MET cc_start: 0.8242 (ttm) cc_final: 0.7949 (tpp) REVERT: D 423 MET cc_start: 0.8477 (pmm) cc_final: 0.7892 (pmm) REVERT: D 443 TYR cc_start: 0.7933 (m-10) cc_final: 0.7645 (m-10) REVERT: D 525 MET cc_start: 0.9060 (ppp) cc_final: 0.8778 (ppp) REVERT: D 696 MET cc_start: 0.9190 (tpp) cc_final: 0.8965 (tpp) REVERT: D 827 LEU cc_start: 0.8861 (tt) cc_final: 0.8660 (tp) REVERT: H 81 ASP cc_start: 0.8405 (t0) cc_final: 0.8041 (t0) REVERT: H 174 TYR cc_start: 0.8255 (p90) cc_final: 0.7546 (p90) REVERT: H 207 GLN cc_start: 0.8146 (tt0) cc_final: 0.7157 (tp40) REVERT: F 99 ARG cc_start: 0.8681 (tpp80) cc_final: 0.8457 (ttm-80) REVERT: F 106 ILE cc_start: 0.8853 (tt) cc_final: 0.8593 (tp) REVERT: F 120 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (tp) REVERT: G 191 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8544 (mm-30) REVERT: E 32 TYR cc_start: 0.8058 (m-80) cc_final: 0.7536 (m-10) REVERT: E 70 GLU cc_start: 0.8444 (mp0) cc_final: 0.8232 (pp20) REVERT: E 82 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.6993 (m170) REVERT: E 95 GLU cc_start: 0.8589 (pm20) cc_final: 0.8290 (pp20) REVERT: E 110 LEU cc_start: 0.9506 (tp) cc_final: 0.9101 (tp) REVERT: E 180 PHE cc_start: 0.8979 (t80) cc_final: 0.8693 (t80) REVERT: B 901 GLU cc_start: 0.6761 (mm-30) cc_final: 0.5368 (tp30) outliers start: 56 outliers final: 50 residues processed: 291 average time/residue: 0.1191 time to fit residues: 55.9603 Evaluate side-chains 299 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 245 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 568 PHE Chi-restraints excluded: chain A residue 730 MET Chi-restraints excluded: chain A residue 731 ASN Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 795 CYS Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 568 PHE Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain C residue 457 HIS Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 766 THR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 568 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain D residue 651 MET Chi-restraints excluded: chain D residue 692 MET Chi-restraints excluded: chain D residue 830 LEU Chi-restraints excluded: chain D residue 833 LEU Chi-restraints excluded: chain H residue 121 CYS Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 77 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 200 MET Chi-restraints excluded: chain G residue 185 LEU Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 65 ARG Chi-restraints excluded: chain E residue 82 HIS Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 102 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 213 optimal weight: 8.9990 chunk 165 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 211 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.102858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077391 restraints weight = 56387.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.078393 restraints weight = 29118.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.078528 restraints weight = 22129.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079082 restraints weight = 20279.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079037 restraints weight = 17977.675| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18527 Z= 0.120 Angle : 0.650 15.283 25042 Z= 0.311 Chirality : 0.041 0.248 2800 Planarity : 0.004 0.051 3056 Dihedral : 5.189 80.122 2596 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 2.65 % Allowed : 20.95 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 1.50 (0.19), residues: 2256 helix: 2.38 (0.15), residues: 1262 sheet: -1.69 (0.41), residues: 146 loop : -0.65 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 765 TYR 0.020 0.001 TYR C 819 PHE 0.013 0.001 PHE C 629 TRP 0.019 0.001 TRP C 788 HIS 0.004 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00270 (18516) covalent geometry : angle 0.64892 (25020) SS BOND : bond 0.00313 ( 11) SS BOND : angle 1.18218 ( 22) hydrogen bonds : bond 0.03513 ( 1077) hydrogen bonds : angle 4.03010 ( 3087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3025.32 seconds wall clock time: 53 minutes 18.45 seconds (3198.45 seconds total)