Starting phenix.real_space_refine on Sun Aug 24 08:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrn_48560/08_2025/9mrn_48560.map" } resolution = 3.46 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= 0.017 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 11885 2.51 5 N 2967 2.21 5 O 3318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18298 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3223 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3236 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 401} Chain breaks: 1 Chain: "D" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3219 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 400} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "F" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "G" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain breaks: 3 Chain: "H" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1336 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 170} 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: "B" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 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} Time building chain proxies: 4.49, per 1000 atoms: 0.25 Number of scatterers: 18298 At special positions: 0 Unit cell: (117.37, 125.13, 146.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3318 8.00 N 2967 7.00 C 11885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 67 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 76 " 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: 1.75 Conformation dependent library (CDL) restraints added in 889.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4276 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 24 sheets defined 57.6% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.728A pdb=" N LEU A 467 " --> pdb=" O MET A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.581A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.585A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 626 removed outlier: 3.607A pdb=" N ALA A 621 " --> pdb=" O THR A 617 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 622 " --> pdb=" O ALA A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 662 Processing helix chain 'A' and resid 664 through 677 Processing helix chain 'A' and resid 685 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 742 through 757 Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.631A pdb=" N LYS A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 4.301A pdb=" N ALA A 775 " --> pdb=" O GLU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 820 removed outlier: 3.685A pdb=" N VAL A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.208A pdb=" N GLU B 413 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.546A pdb=" N LEU B 467 " --> pdb=" O MET B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 544 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 615 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.629A pdb=" N LYS B 641 " --> pdb=" O GLU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 Processing helix chain 'B' and resid 664 through 677 Processing helix chain 'B' and resid 685 through 696 Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 Processing helix chain 'B' and resid 757 through 768 Processing helix chain 'B' and resid 788 through 818 removed outlier: 3.833A pdb=" N VAL B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 798 " --> pdb=" O GLY B 794 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 461 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.630A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.533A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.585A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 626 removed outlier: 3.501A pdb=" N ALA C 621 " --> pdb=" O THR C 617 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 622 " --> pdb=" O ALA C 618 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 653 through 662 Processing helix chain 'C' and resid 664 through 677 Processing helix chain 'C' and resid 685 through 696 Processing helix chain 'C' and resid 706 through 715 removed outlier: 3.534A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 757 removed outlier: 3.609A pdb=" N LEU C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.613A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 820 removed outlier: 3.696A pdb=" N VAL C 792 " --> pdb=" O SER C 788 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.657A pdb=" N LEU D 467 " --> pdb=" O MET D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 544 Processing helix chain 'D' and resid 572 through 586 Processing helix chain 'D' and resid 595 through 614 Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 637 through 642 removed outlier: 3.752A pdb=" N LYS D 641 " --> pdb=" O GLU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.501A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 675 Processing helix chain 'D' and resid 685 through 696 Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 773 through 781 removed outlier: 4.131A pdb=" N SER D 778 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLY D 779 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 819 removed outlier: 3.784A pdb=" N VAL D 792 " --> pdb=" O SER D 788 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 819 " --> pdb=" O CYS D 815 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 28 removed outlier: 3.768A pdb=" N LEU E 10 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 104 through 125 removed outlier: 3.680A pdb=" N ILE E 108 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU E 125 " --> pdb=" O ILE E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 161 removed outlier: 4.099A pdb=" N LEU E 135 " --> pdb=" O HIS E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 207 removed outlier: 3.832A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 28 removed outlier: 3.742A pdb=" N LEU F 10 " --> pdb=" O GLY F 6 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 28 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 104 through 126 removed outlier: 3.866A pdb=" N ILE F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 161 Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.767A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 28 removed outlier: 3.871A pdb=" N LEU G 10 " --> pdb=" O GLY G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 104 through 125 removed outlier: 3.785A pdb=" N ILE G 108 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 160 removed outlier: 3.543A pdb=" N SER G 136 " --> pdb=" O ASN G 132 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA G 160 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.882A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 207 " --> pdb=" O ARG G 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 28 removed outlier: 3.606A pdb=" N GLY H 28 " --> pdb=" O THR H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.913A pdb=" N ILE H 108 " --> pdb=" O SER H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 161 Processing helix chain 'H' and resid 176 through 204 removed outlier: 3.755A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 441 removed outlier: 6.260A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 474 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.139A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.213A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 702 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 503 " --> pdb=" O TYR A 702 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 723 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 440 through 444 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.927A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 646 through 649 removed outlier: 6.474A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 441 removed outlier: 6.196A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 474 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.123A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.265A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR C 702 " --> pdb=" O MET C 503 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 723 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 439 through 444 removed outlier: 6.201A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR D 443 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.931A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 646 through 649 removed outlier: 6.443A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 33 through 36 removed outlier: 3.926A pdb=" N MET E 57 " --> pdb=" O LEU E 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 76 through 78 removed outlier: 3.889A pdb=" N MET F 57 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER F 174 " --> pdb=" O TYR F 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 33 through 36 Processing sheet with id=AC6, first strand: chain 'H' and resid 76 through 78 removed outlier: 3.772A pdb=" N MET H 57 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER H 174 " --> pdb=" O TYR H 34 " (cutoff:3.500A) 1047 hydrogen bonds defined for protein. 3063 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: 3.31 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5617 1.34 - 1.46: 4484 1.46 - 1.58: 8381 1.58 - 1.70: 0 1.70 - 1.82: 208 Bond restraints: 18690 Sorted by residual: bond pdb=" N ILE B 612 " pdb=" CA ILE B 612 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.46e+00 bond pdb=" N ILE D 613 " pdb=" CA ILE D 613 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.90e+00 bond pdb=" N VAL C 626 " pdb=" CA VAL C 626 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.41e+00 bond pdb=" N ILE C 613 " pdb=" CA ILE C 613 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.37e+00 bond pdb=" N ILE B 613 " pdb=" CA ILE B 613 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.14e-02 7.69e+03 8.21e+00 ... (remaining 18685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 24401 1.89 - 3.79: 697 3.79 - 5.68: 87 5.68 - 7.58: 19 7.58 - 9.47: 6 Bond angle restraints: 25210 Sorted by residual: angle pdb=" N TYR D 616 " pdb=" CA TYR D 616 " pdb=" C TYR D 616 " ideal model delta sigma weight residual 114.04 106.54 7.50 1.24e+00 6.50e-01 3.66e+01 angle pdb=" N TYR B 616 " pdb=" CA TYR B 616 " pdb=" C TYR B 616 " ideal model delta sigma weight residual 114.04 106.65 7.39 1.24e+00 6.50e-01 3.55e+01 angle pdb=" N LEU C 624 " pdb=" CA LEU C 624 " pdb=" C LEU C 624 " ideal model delta sigma weight residual 113.97 108.17 5.80 1.28e+00 6.10e-01 2.05e+01 angle pdb=" CA THR C 617 " pdb=" CB THR C 617 " pdb=" OG1 THR C 617 " ideal model delta sigma weight residual 109.60 103.47 6.13 1.50e+00 4.44e-01 1.67e+01 angle pdb=" CA THR D 617 " pdb=" CB THR D 617 " pdb=" OG1 THR D 617 " ideal model delta sigma weight residual 109.60 103.77 5.83 1.50e+00 4.44e-01 1.51e+01 ... (remaining 25205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 10243 17.58 - 35.17: 587 35.17 - 52.75: 108 52.75 - 70.33: 33 70.33 - 87.92: 9 Dihedral angle restraints: 10980 sinusoidal: 4274 harmonic: 6706 Sorted by residual: dihedral pdb=" CA ASN C 461 " pdb=" C ASN C 461 " pdb=" N GLY C 462 " pdb=" CA GLY C 462 " ideal model delta harmonic sigma weight residual -180.00 -140.98 -39.02 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" CB CYS C 718 " pdb=" SG CYS C 718 " pdb=" SG CYS C 773 " pdb=" CB CYS C 773 " ideal model delta sinusoidal sigma weight residual 93.00 159.33 -66.33 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS D 718 " pdb=" SG CYS D 718 " pdb=" SG CYS D 773 " pdb=" CB CYS D 773 " ideal model delta sinusoidal sigma weight residual 93.00 146.63 -53.63 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 10977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1954 0.045 - 0.089: 673 0.089 - 0.134: 154 0.134 - 0.178: 36 0.178 - 0.223: 9 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CA THR C 744 " pdb=" N THR C 744 " pdb=" C THR C 744 " pdb=" CB THR C 744 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLU A 627 " pdb=" N GLU A 627 " pdb=" C GLU A 627 " pdb=" CB GLU A 627 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 2823 not shown) Planarity restraints: 3106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 647 " -0.003 2.00e-02 2.50e+03 2.03e-02 8.26e+00 pdb=" CG TYR D 647 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR D 647 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR D 647 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 647 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR D 647 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 647 " 0.029 2.00e-02 2.50e+03 pdb=" OH TYR D 647 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 647 " 0.004 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR B 647 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 647 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 647 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 647 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B 647 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 647 " -0.027 2.00e-02 2.50e+03 pdb=" OH TYR B 647 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 661 " 0.202 9.50e-02 1.11e+02 9.15e-02 6.84e+00 pdb=" NE ARG B 661 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG B 661 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG B 661 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 661 " -0.000 2.00e-02 2.50e+03 ... (remaining 3103 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3909 2.79 - 3.31: 17973 3.31 - 3.84: 27491 3.84 - 4.37: 30536 4.37 - 4.90: 55401 Nonbonded interactions: 135310 Sorted by model distance: nonbonded pdb=" OG SER B 592 " pdb=" OD2 ASP C 590 " model vdw 2.256 3.040 nonbonded pdb=" O ARG C 692 " pdb=" OG SER C 696 " model vdw 2.273 3.040 nonbonded pdb=" O ARG A 692 " pdb=" OG SER A 696 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP C 454 " pdb=" OG1 THR C 457 " model vdw 2.306 3.040 nonbonded pdb=" OE2 GLU D 637 " pdb=" OG SER D 640 " model vdw 2.341 3.040 ... (remaining 135305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = (chain 'B' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 1301)) selection = (chain 'C' and (resid 391 through 504 or (resid 505 and (name N or name CA or na \ me C or name O or name CB )) or resid 506 through 817 or (resid 818 through 819 \ and (name N or name CA or name C or name O or name CB )) or resid 1301)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.090 Find NCS groups from input model: 0.410 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: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.005 0.063 18702 Z= 0.260 Angle : 0.774 9.470 25234 Z= 0.480 Chirality : 0.048 0.223 2826 Planarity : 0.008 0.091 3106 Dihedral : 12.206 87.915 6668 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 0.56 % Allowed : 0.82 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -0.30 (0.16), residues: 2298 helix: 0.51 (0.13), residues: 1270 sheet: 0.03 (0.37), residues: 176 loop : -1.25 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG B 661 TYR 0.036 0.003 TYR C 732 PHE 0.036 0.002 PHE A 574 TRP 0.031 0.003 TRP F 177 HIS 0.005 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00529 (18690) covalent geometry : angle 0.77344 (25210) SS BOND : bond 0.00259 ( 12) SS BOND : angle 1.01018 ( 24) hydrogen bonds : bond 0.17378 ( 1047) hydrogen bonds : angle 6.06702 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 463 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 714 GLN cc_start: 0.7163 (mm-40) cc_final: 0.6932 (mm-40) REVERT: A 721 MET cc_start: 0.7133 (ttm) cc_final: 0.6848 (tpp) REVERT: B 467 LEU cc_start: 0.7861 (mt) cc_final: 0.7585 (mt) REVERT: B 503 MET cc_start: 0.8627 (ttm) cc_final: 0.8391 (ttp) REVERT: C 585 MET cc_start: 0.9136 (mmt) cc_final: 0.7871 (mmt) REVERT: C 624 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8095 (tp) REVERT: C 670 MET cc_start: 0.9205 (mtp) cc_final: 0.8976 (mtp) REVERT: C 702 TYR cc_start: 0.7733 (t80) cc_final: 0.7497 (t80) REVERT: C 721 MET cc_start: 0.7261 (ttt) cc_final: 0.6944 (tpp) REVERT: D 467 LEU cc_start: 0.7820 (mt) cc_final: 0.7540 (mt) REVERT: D 594 ARG cc_start: 0.8564 (ptm160) cc_final: 0.8121 (ttp80) REVERT: E 97 LEU cc_start: 0.8410 (tt) cc_final: 0.8190 (tp) REVERT: E 116 MET cc_start: 0.8276 (mmm) cc_final: 0.7962 (mtm) REVERT: E 202 ASP cc_start: 0.8311 (t70) cc_final: 0.7965 (t70) REVERT: F 125 GLU cc_start: 0.7601 (tp30) cc_final: 0.7116 (tm-30) REVERT: F 202 ASP cc_start: 0.7999 (t70) cc_final: 0.7319 (m-30) REVERT: G 116 MET cc_start: 0.8420 (mmm) cc_final: 0.8082 (mtt) REVERT: G 173 TYR cc_start: 0.8774 (p90) cc_final: 0.7557 (p90) REVERT: G 202 ASP cc_start: 0.7921 (t70) cc_final: 0.7700 (t70) REVERT: H 130 ARG cc_start: 0.6042 (mtt180) cc_final: 0.5746 (mmm160) outliers start: 11 outliers final: 5 residues processed: 470 average time/residue: 0.1862 time to fit residues: 121.6704 Evaluate side-chains 269 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain D residue 619 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 619 ASN D 756 GLN F 159 ASN F 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.169260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.130371 restraints weight = 25804.109| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.48 r_work: 0.3088 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18702 Z= 0.164 Angle : 0.603 8.208 25234 Z= 0.328 Chirality : 0.042 0.168 2826 Planarity : 0.004 0.057 3106 Dihedral : 5.471 61.486 2537 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.52 % Favored : 97.35 % Rotamer: Outliers : 1.99 % Allowed : 8.59 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.52 (0.18), residues: 2298 helix: 2.41 (0.14), residues: 1272 sheet: -0.05 (0.34), residues: 194 loop : -1.00 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 203 TYR 0.020 0.002 TYR F 127 PHE 0.017 0.002 PHE A 574 TRP 0.019 0.002 TRP H 177 HIS 0.003 0.001 HIS E 131 Details of bonding type rmsd covalent geometry : bond 0.00370 (18690) covalent geometry : angle 0.60302 (25210) SS BOND : bond 0.00230 ( 12) SS BOND : angle 0.87941 ( 24) hydrogen bonds : bond 0.07381 ( 1047) hydrogen bonds : angle 4.32779 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 281 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7768 (mmt) cc_final: 0.7498 (mmt) REVERT: A 721 MET cc_start: 0.7521 (ttm) cc_final: 0.7148 (tpp) REVERT: B 414 MET cc_start: 0.5879 (mpp) cc_final: 0.5463 (ptp) REVERT: B 503 MET cc_start: 0.8559 (ttm) cc_final: 0.8187 (ttp) REVERT: B 628 ARG cc_start: 0.8452 (pmt-80) cc_final: 0.8221 (ppt170) REVERT: C 414 MET cc_start: 0.7106 (mpp) cc_final: 0.6660 (ptp) REVERT: C 463 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6954 (mtp) REVERT: C 721 MET cc_start: 0.7554 (ttt) cc_final: 0.7327 (tpt) REVERT: D 594 ARG cc_start: 0.8702 (ptm160) cc_final: 0.8317 (ttp80) REVERT: E 17 PHE cc_start: 0.8927 (t80) cc_final: 0.8505 (t80) REVERT: E 29 THR cc_start: 0.8420 (m) cc_final: 0.8081 (m) REVERT: E 98 ARG cc_start: 0.7729 (mtt90) cc_final: 0.7469 (mtt90) REVERT: E 116 MET cc_start: 0.8026 (mmm) cc_final: 0.7779 (mtm) REVERT: E 202 ASP cc_start: 0.8263 (t70) cc_final: 0.7967 (t70) REVERT: F 94 GLU cc_start: 0.7998 (pm20) cc_final: 0.7543 (pt0) REVERT: F 125 GLU cc_start: 0.7463 (tp30) cc_final: 0.7182 (tp30) REVERT: F 128 LYS cc_start: 0.7333 (mptt) cc_final: 0.6683 (tptt) REVERT: F 202 ASP cc_start: 0.8068 (t70) cc_final: 0.7321 (m-30) REVERT: G 17 PHE cc_start: 0.8945 (t80) cc_final: 0.8503 (t80) REVERT: G 29 THR cc_start: 0.8441 (m) cc_final: 0.8116 (m) REVERT: G 116 MET cc_start: 0.8106 (mmm) cc_final: 0.7808 (mtm) REVERT: G 173 TYR cc_start: 0.8848 (p90) cc_final: 0.7575 (p90) REVERT: G 202 ASP cc_start: 0.8085 (t70) cc_final: 0.7814 (t70) REVERT: H 121 ILE cc_start: 0.8158 (mm) cc_final: 0.7954 (tt) REVERT: H 130 ARG cc_start: 0.6174 (mtt180) cc_final: 0.5657 (mmm160) outliers start: 39 outliers final: 24 residues processed: 307 average time/residue: 0.1669 time to fit residues: 73.3389 Evaluate side-chains 261 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 51 optimal weight: 0.0020 chunk 211 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 188 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN H 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126797 restraints weight = 25974.542| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.60 r_work: 0.3029 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18702 Z= 0.183 Angle : 0.587 8.519 25234 Z= 0.318 Chirality : 0.042 0.172 2826 Planarity : 0.004 0.052 3106 Dihedral : 5.046 56.776 2529 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.87 % Favored : 97.00 % Rotamer: Outliers : 2.92 % Allowed : 10.59 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.65 (0.18), residues: 2298 helix: 2.64 (0.15), residues: 1274 sheet: -0.16 (0.36), residues: 174 loop : -1.13 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 675 TYR 0.017 0.002 TYR C 424 PHE 0.017 0.002 PHE A 495 TRP 0.016 0.002 TRP H 177 HIS 0.024 0.002 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00429 (18690) covalent geometry : angle 0.58641 (25210) SS BOND : bond 0.00349 ( 12) SS BOND : angle 0.79055 ( 24) hydrogen bonds : bond 0.07883 ( 1047) hydrogen bonds : angle 4.19938 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 250 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8487 (pp) REVERT: A 700 TYR cc_start: 0.5587 (t80) cc_final: 0.5279 (t80) REVERT: A 721 MET cc_start: 0.7581 (ttm) cc_final: 0.7314 (tpp) REVERT: B 628 ARG cc_start: 0.8441 (pmt-80) cc_final: 0.8217 (ppt170) REVERT: C 414 MET cc_start: 0.7197 (mpp) cc_final: 0.6647 (ptt) REVERT: C 673 TYR cc_start: 0.8581 (t80) cc_final: 0.8205 (t80) REVERT: D 405 TYR cc_start: 0.8806 (m-10) cc_final: 0.8578 (m-80) REVERT: D 594 ARG cc_start: 0.8845 (ptm160) cc_final: 0.8441 (ttp80) REVERT: D 756 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: E 17 PHE cc_start: 0.8936 (t80) cc_final: 0.8562 (t80) REVERT: E 29 THR cc_start: 0.8456 (m) cc_final: 0.8132 (m) REVERT: E 36 ARG cc_start: 0.7215 (mtp-110) cc_final: 0.6869 (mtp-110) REVERT: E 73 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8998 (ttmt) REVERT: E 202 ASP cc_start: 0.8374 (t70) cc_final: 0.8057 (t70) REVERT: F 36 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: F 94 GLU cc_start: 0.8115 (pm20) cc_final: 0.7695 (pt0) REVERT: F 202 ASP cc_start: 0.8121 (t70) cc_final: 0.7439 (m-30) REVERT: G 17 PHE cc_start: 0.8987 (t80) cc_final: 0.8562 (t80) REVERT: G 29 THR cc_start: 0.8487 (m) cc_final: 0.8141 (m) REVERT: G 36 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.6929 (mmm-85) REVERT: G 116 MET cc_start: 0.8143 (mmm) cc_final: 0.7938 (mtt) REVERT: G 173 TYR cc_start: 0.8857 (p90) cc_final: 0.7643 (p90) REVERT: G 202 ASP cc_start: 0.8077 (t70) cc_final: 0.7828 (t70) REVERT: H 58 THR cc_start: 0.8727 (p) cc_final: 0.8263 (t) REVERT: H 116 MET cc_start: 0.8838 (mmm) cc_final: 0.8560 (mtt) REVERT: H 130 ARG cc_start: 0.6330 (mtt180) cc_final: 0.5752 (mmm160) REVERT: H 202 ASP cc_start: 0.7827 (t0) cc_final: 0.6808 (m-30) outliers start: 57 outliers final: 42 residues processed: 286 average time/residue: 0.1562 time to fit residues: 64.9777 Evaluate side-chains 271 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 217 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.3980 chunk 120 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN F 204 HIS ** G 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.165669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127253 restraints weight = 25918.646| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 4.44 r_work: 0.3017 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18702 Z= 0.171 Angle : 0.554 8.497 25234 Z= 0.301 Chirality : 0.041 0.157 2826 Planarity : 0.004 0.050 3106 Dihedral : 4.839 52.883 2529 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.87 % Favored : 97.00 % Rotamer: Outliers : 3.32 % Allowed : 11.66 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.51 (0.18), residues: 2298 helix: 2.61 (0.15), residues: 1290 sheet: -0.19 (0.42), residues: 138 loop : -1.41 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 675 TYR 0.016 0.001 TYR C 424 PHE 0.016 0.002 PHE D 546 TRP 0.013 0.001 TRP H 177 HIS 0.004 0.001 HIS E 59 Details of bonding type rmsd covalent geometry : bond 0.00397 (18690) covalent geometry : angle 0.55425 (25210) SS BOND : bond 0.00353 ( 12) SS BOND : angle 0.73339 ( 24) hydrogen bonds : bond 0.07472 ( 1047) hydrogen bonds : angle 4.05324 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 236 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6198 (mp0) REVERT: A 673 TYR cc_start: 0.8638 (t80) cc_final: 0.8369 (t80) REVERT: B 628 ARG cc_start: 0.8528 (pmt-80) cc_final: 0.8321 (ppt170) REVERT: C 600 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (mt) REVERT: C 657 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: C 673 TYR cc_start: 0.8549 (t80) cc_final: 0.8179 (t80) REVERT: D 414 MET cc_start: 0.7510 (ptm) cc_final: 0.7300 (tmm) REVERT: D 421 TYR cc_start: 0.7272 (m-80) cc_final: 0.6912 (m-80) REVERT: D 439 LYS cc_start: 0.7213 (ptpt) cc_final: 0.6766 (mmmt) REVERT: D 594 ARG cc_start: 0.8895 (ptm160) cc_final: 0.8456 (ttp80) REVERT: E 29 THR cc_start: 0.8526 (m) cc_final: 0.8230 (m) REVERT: E 36 ARG cc_start: 0.7230 (mtp-110) cc_final: 0.6904 (mtp-110) REVERT: E 57 MET cc_start: 0.6514 (mmp) cc_final: 0.6065 (mmp) REVERT: E 98 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7584 (mtt90) REVERT: E 202 ASP cc_start: 0.8443 (t70) cc_final: 0.8059 (t70) REVERT: F 36 ARG cc_start: 0.7992 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: F 94 GLU cc_start: 0.8170 (pm20) cc_final: 0.7783 (pt0) REVERT: F 128 LYS cc_start: 0.7213 (mptt) cc_final: 0.6422 (tptt) REVERT: F 202 ASP cc_start: 0.8157 (t70) cc_final: 0.7488 (m-30) REVERT: G 17 PHE cc_start: 0.9002 (t80) cc_final: 0.8640 (t80) REVERT: G 29 THR cc_start: 0.8417 (m) cc_final: 0.8099 (m) REVERT: G 36 ARG cc_start: 0.7466 (mmm-85) cc_final: 0.7142 (mmm-85) REVERT: G 98 ARG cc_start: 0.7772 (mtt90) cc_final: 0.7511 (mtt90) REVERT: G 202 ASP cc_start: 0.8154 (t70) cc_final: 0.7929 (t70) REVERT: H 58 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8332 (t) REVERT: H 94 GLU cc_start: 0.8129 (pm20) cc_final: 0.7574 (pt0) REVERT: H 116 MET cc_start: 0.8884 (mmm) cc_final: 0.8676 (mtt) REVERT: H 121 ILE cc_start: 0.8200 (tt) cc_final: 0.7996 (tt) REVERT: H 130 ARG cc_start: 0.6313 (mtt180) cc_final: 0.5768 (mmm160) REVERT: H 202 ASP cc_start: 0.7871 (t0) cc_final: 0.6942 (m-30) outliers start: 65 outliers final: 53 residues processed: 275 average time/residue: 0.1367 time to fit residues: 55.1824 Evaluate side-chains 286 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 229 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 527 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 600 ILE Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 817 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 ILE Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 40 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN E 204 HIS F 204 HIS G 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.131856 restraints weight = 25862.126| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.44 r_work: 0.3055 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18702 Z= 0.138 Angle : 0.515 8.612 25234 Z= 0.277 Chirality : 0.039 0.152 2826 Planarity : 0.004 0.046 3106 Dihedral : 4.573 48.987 2529 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 3.27 % Allowed : 12.38 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.66 (0.18), residues: 2298 helix: 2.78 (0.15), residues: 1290 sheet: -0.03 (0.41), residues: 156 loop : -1.45 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 675 TYR 0.013 0.001 TYR A 700 PHE 0.013 0.001 PHE D 546 TRP 0.011 0.001 TRP H 177 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00308 (18690) covalent geometry : angle 0.51474 (25210) SS BOND : bond 0.00151 ( 12) SS BOND : angle 0.67843 ( 24) hydrogen bonds : bond 0.06562 ( 1047) hydrogen bonds : angle 3.84912 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 244 time to evaluate : 0.652 Fit side-chains REVERT: A 498 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8471 (pp) REVERT: A 657 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6143 (mp0) REVERT: A 673 TYR cc_start: 0.8630 (t80) cc_final: 0.8321 (t80) REVERT: B 521 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 657 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: C 673 TYR cc_start: 0.8509 (t80) cc_final: 0.8079 (t80) REVERT: C 708 MET cc_start: 0.8650 (mmt) cc_final: 0.7811 (mtt) REVERT: D 414 MET cc_start: 0.7538 (ptm) cc_final: 0.7277 (tmm) REVERT: D 421 TYR cc_start: 0.7262 (m-80) cc_final: 0.6978 (m-80) REVERT: D 439 LYS cc_start: 0.7137 (ptpt) cc_final: 0.6684 (mmmt) REVERT: D 756 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: D 766 TRP cc_start: 0.8153 (m100) cc_final: 0.7943 (m100) REVERT: E 17 PHE cc_start: 0.8897 (t80) cc_final: 0.8585 (t80) REVERT: E 29 THR cc_start: 0.8322 (m) cc_final: 0.8002 (m) REVERT: E 36 ARG cc_start: 0.7256 (mtp-110) cc_final: 0.6907 (mtp-110) REVERT: E 57 MET cc_start: 0.6598 (mmp) cc_final: 0.6163 (mmp) REVERT: E 98 ARG cc_start: 0.7771 (mtt90) cc_final: 0.7445 (mtt90) REVERT: E 202 ASP cc_start: 0.8402 (t70) cc_final: 0.8052 (t70) REVERT: F 58 THR cc_start: 0.8771 (p) cc_final: 0.8324 (t) REVERT: F 94 GLU cc_start: 0.8139 (pm20) cc_final: 0.7803 (pt0) REVERT: F 128 LYS cc_start: 0.7166 (mptt) cc_final: 0.6397 (tptt) REVERT: F 202 ASP cc_start: 0.8140 (t70) cc_final: 0.7485 (m-30) REVERT: G 11 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6977 (mt) REVERT: G 17 PHE cc_start: 0.8933 (t80) cc_final: 0.8524 (t80) REVERT: G 29 THR cc_start: 0.8267 (m) cc_final: 0.7942 (m) REVERT: G 36 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.6880 (mmm-85) REVERT: G 98 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7523 (mtt90) REVERT: G 173 TYR cc_start: 0.8853 (p90) cc_final: 0.7657 (p90) REVERT: G 202 ASP cc_start: 0.8048 (t70) cc_final: 0.7822 (t70) REVERT: H 58 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8223 (t) REVERT: H 94 GLU cc_start: 0.8129 (pm20) cc_final: 0.7614 (pt0) REVERT: H 116 MET cc_start: 0.8818 (mmm) cc_final: 0.8611 (mtt) REVERT: H 121 ILE cc_start: 0.8136 (tt) cc_final: 0.7882 (tt) REVERT: H 130 ARG cc_start: 0.6190 (mtt180) cc_final: 0.5625 (mmm160) outliers start: 64 outliers final: 48 residues processed: 283 average time/residue: 0.1376 time to fit residues: 57.6809 Evaluate side-chains 287 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 232 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 619 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 159 optimal weight: 0.0270 chunk 9 optimal weight: 0.0170 chunk 134 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 45 optimal weight: 0.9980 chunk 210 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 587 GLN D 756 GLN G 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.173021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137739 restraints weight = 25968.565| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.90 r_work: 0.3193 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18702 Z= 0.102 Angle : 0.479 8.169 25234 Z= 0.254 Chirality : 0.038 0.154 2826 Planarity : 0.003 0.038 3106 Dihedral : 4.101 41.444 2529 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.96 % Favored : 97.91 % Rotamer: Outliers : 2.92 % Allowed : 13.45 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.99 (0.18), residues: 2298 helix: 3.13 (0.15), residues: 1278 sheet: 0.06 (0.48), residues: 120 loop : -1.34 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 675 TYR 0.014 0.001 TYR A 700 PHE 0.016 0.001 PHE D 546 TRP 0.009 0.001 TRP C 766 HIS 0.028 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00203 (18690) covalent geometry : angle 0.47884 (25210) SS BOND : bond 0.00245 ( 12) SS BOND : angle 0.63961 ( 24) hydrogen bonds : bond 0.04407 ( 1047) hydrogen bonds : angle 3.48679 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 253 time to evaluate : 0.651 Fit side-chains REVERT: A 657 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6087 (mp0) REVERT: A 673 TYR cc_start: 0.8621 (t80) cc_final: 0.8375 (t80) REVERT: A 721 MET cc_start: 0.7217 (tpp) cc_final: 0.6967 (tpp) REVERT: B 421 TYR cc_start: 0.7162 (m-80) cc_final: 0.6797 (m-80) REVERT: B 521 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8380 (mp) REVERT: C 657 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: C 673 TYR cc_start: 0.8495 (t80) cc_final: 0.8151 (t80) REVERT: C 708 MET cc_start: 0.8576 (mmt) cc_final: 0.7826 (mtm) REVERT: D 402 GLU cc_start: 0.8488 (tp30) cc_final: 0.8172 (tp30) REVERT: D 414 MET cc_start: 0.7622 (ptm) cc_final: 0.7297 (tmm) REVERT: D 439 LYS cc_start: 0.7021 (ptpt) cc_final: 0.6670 (mmmt) REVERT: D 638 ASP cc_start: 0.7197 (m-30) cc_final: 0.6357 (t0) REVERT: E 11 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6854 (mt) REVERT: E 17 PHE cc_start: 0.8848 (t80) cc_final: 0.8482 (t80) REVERT: E 36 ARG cc_start: 0.7186 (mtp-110) cc_final: 0.6854 (mtp-110) REVERT: E 57 MET cc_start: 0.6606 (mmp) cc_final: 0.6242 (mmp) REVERT: E 98 ARG cc_start: 0.7684 (mtt90) cc_final: 0.7392 (mtt90) REVERT: E 202 ASP cc_start: 0.8324 (t70) cc_final: 0.7984 (t70) REVERT: F 58 THR cc_start: 0.8666 (p) cc_final: 0.8230 (t) REVERT: F 94 GLU cc_start: 0.8041 (pm20) cc_final: 0.7838 (pt0) REVERT: F 128 LYS cc_start: 0.7081 (mptt) cc_final: 0.6281 (tptt) REVERT: F 198 HIS cc_start: 0.7415 (t70) cc_final: 0.6844 (m-70) REVERT: F 202 ASP cc_start: 0.8001 (t70) cc_final: 0.7800 (t0) REVERT: F 204 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6689 (t-90) REVERT: G 11 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7000 (mt) REVERT: G 17 PHE cc_start: 0.8843 (t80) cc_final: 0.8406 (t80) REVERT: G 36 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.6866 (mmm-85) REVERT: G 40 LYS cc_start: 0.5895 (tttm) cc_final: 0.5631 (ttpt) REVERT: G 98 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7430 (mtt90) REVERT: G 173 TYR cc_start: 0.8866 (p90) cc_final: 0.7630 (p90) REVERT: G 202 ASP cc_start: 0.7830 (t70) cc_final: 0.7622 (t70) REVERT: H 58 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8096 (t) REVERT: H 94 GLU cc_start: 0.8097 (pm20) cc_final: 0.7671 (pt0) REVERT: H 130 ARG cc_start: 0.6041 (mtt180) cc_final: 0.5587 (mmm160) outliers start: 57 outliers final: 32 residues processed: 295 average time/residue: 0.1364 time to fit residues: 60.0865 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 158 optimal weight: 4.9990 chunk 212 optimal weight: 0.6980 chunk 221 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 173 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN F 204 HIS G 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.168152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130967 restraints weight = 25861.672| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.30 r_work: 0.3095 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18702 Z= 0.133 Angle : 0.505 8.253 25234 Z= 0.270 Chirality : 0.039 0.245 2826 Planarity : 0.003 0.041 3106 Dihedral : 4.073 37.055 2527 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 2.71 % Allowed : 14.22 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.87 (0.18), residues: 2298 helix: 3.07 (0.15), residues: 1280 sheet: -0.11 (0.44), residues: 132 loop : -1.46 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 675 TYR 0.013 0.001 TYR C 450 PHE 0.013 0.001 PHE A 495 TRP 0.008 0.001 TRP H 177 HIS 0.005 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00302 (18690) covalent geometry : angle 0.50459 (25210) SS BOND : bond 0.00130 ( 12) SS BOND : angle 0.56610 ( 24) hydrogen bonds : bond 0.05965 ( 1047) hydrogen bonds : angle 3.65400 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.679 Fit side-chains REVERT: A 458 LYS cc_start: 0.7296 (tppt) cc_final: 0.7089 (tppt) REVERT: A 657 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6196 (mp0) REVERT: A 673 TYR cc_start: 0.8632 (t80) cc_final: 0.8385 (t80) REVERT: B 421 TYR cc_start: 0.7199 (m-80) cc_final: 0.6840 (m-80) REVERT: B 521 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8720 (mp) REVERT: C 657 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: C 673 TYR cc_start: 0.8500 (t80) cc_final: 0.8193 (t80) REVERT: D 756 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7479 (mt0) REVERT: E 17 PHE cc_start: 0.8985 (t80) cc_final: 0.8645 (t80) REVERT: E 29 THR cc_start: 0.8070 (m) cc_final: 0.7797 (m) REVERT: E 36 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.7025 (mtp-110) REVERT: E 202 ASP cc_start: 0.8408 (t70) cc_final: 0.8061 (t70) REVERT: F 58 THR cc_start: 0.8752 (p) cc_final: 0.8306 (t) REVERT: F 128 LYS cc_start: 0.7194 (mptt) cc_final: 0.6423 (tptt) REVERT: F 198 HIS cc_start: 0.7538 (t70) cc_final: 0.6997 (m-70) REVERT: G 11 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6976 (mt) REVERT: G 17 PHE cc_start: 0.8946 (t80) cc_final: 0.8531 (t80) REVERT: G 29 THR cc_start: 0.8063 (m) cc_final: 0.7802 (m) REVERT: G 36 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.7057 (mmm-85) REVERT: G 40 LYS cc_start: 0.6109 (tttm) cc_final: 0.5885 (ttpt) REVERT: G 173 TYR cc_start: 0.8889 (p90) cc_final: 0.7723 (p90) REVERT: G 202 ASP cc_start: 0.7962 (t70) cc_final: 0.7704 (t0) REVERT: H 58 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8195 (t) REVERT: H 94 GLU cc_start: 0.8080 (pm20) cc_final: 0.7728 (pt0) REVERT: H 130 ARG cc_start: 0.6057 (mtt180) cc_final: 0.5541 (mmm160) outliers start: 53 outliers final: 41 residues processed: 283 average time/residue: 0.1383 time to fit residues: 58.0781 Evaluate side-chains 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 421 TYR Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 159 ASN Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 201 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN G 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130764 restraints weight = 26058.090| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 4.48 r_work: 0.3077 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18702 Z= 0.134 Angle : 0.505 8.345 25234 Z= 0.270 Chirality : 0.039 0.214 2826 Planarity : 0.003 0.046 3106 Dihedral : 4.071 39.156 2527 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.39 % Favored : 97.48 % Rotamer: Outliers : 2.86 % Allowed : 14.17 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.83 (0.18), residues: 2298 helix: 3.05 (0.15), residues: 1280 sheet: -0.22 (0.43), residues: 144 loop : -1.50 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 675 TYR 0.017 0.001 TYR A 700 PHE 0.012 0.001 PHE A 495 TRP 0.015 0.001 TRP D 766 HIS 0.009 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00304 (18690) covalent geometry : angle 0.50470 (25210) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.62201 ( 24) hydrogen bonds : bond 0.06045 ( 1047) hydrogen bonds : angle 3.65811 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: A 673 TYR cc_start: 0.8629 (t80) cc_final: 0.8375 (t80) REVERT: A 721 MET cc_start: 0.7530 (mtp) cc_final: 0.7043 (mtp) REVERT: B 421 TYR cc_start: 0.7156 (m-80) cc_final: 0.6809 (m-80) REVERT: C 498 LEU cc_start: 0.8069 (pt) cc_final: 0.7752 (pt) REVERT: C 657 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6338 (mp0) REVERT: C 673 TYR cc_start: 0.8481 (t80) cc_final: 0.8164 (t80) REVERT: D 638 ASP cc_start: 0.7314 (m-30) cc_final: 0.6418 (t0) REVERT: E 17 PHE cc_start: 0.8946 (t80) cc_final: 0.8634 (t80) REVERT: E 29 THR cc_start: 0.8157 (m) cc_final: 0.7866 (m) REVERT: E 36 ARG cc_start: 0.7432 (mtp-110) cc_final: 0.6966 (mtp-110) REVERT: E 57 MET cc_start: 0.6708 (mmp) cc_final: 0.6351 (mmp) REVERT: E 98 ARG cc_start: 0.7732 (mtt90) cc_final: 0.7413 (mtt90) REVERT: E 202 ASP cc_start: 0.8406 (t70) cc_final: 0.8060 (t70) REVERT: F 58 THR cc_start: 0.8739 (p) cc_final: 0.8289 (t) REVERT: F 128 LYS cc_start: 0.7222 (mptt) cc_final: 0.6422 (tptt) REVERT: F 198 HIS cc_start: 0.7419 (t70) cc_final: 0.6897 (m-70) REVERT: G 11 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6936 (mt) REVERT: G 17 PHE cc_start: 0.8913 (t80) cc_final: 0.8551 (t80) REVERT: G 29 THR cc_start: 0.8173 (m) cc_final: 0.7881 (m) REVERT: G 36 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.7065 (mmm-85) REVERT: G 40 LYS cc_start: 0.5943 (tttm) cc_final: 0.5729 (ttpt) REVERT: G 98 ARG cc_start: 0.7688 (mtt90) cc_final: 0.7348 (mtt90) REVERT: G 173 TYR cc_start: 0.8922 (p90) cc_final: 0.7714 (p90) REVERT: G 202 ASP cc_start: 0.8027 (t70) cc_final: 0.7732 (t0) REVERT: H 58 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8170 (t) REVERT: H 94 GLU cc_start: 0.8050 (pm20) cc_final: 0.7698 (pt0) REVERT: H 130 ARG cc_start: 0.6011 (mtt180) cc_final: 0.5475 (mmm160) outliers start: 56 outliers final: 49 residues processed: 267 average time/residue: 0.1464 time to fit residues: 58.6731 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 229 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 721 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 421 TYR Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 174 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 36 optimal weight: 0.0370 chunk 98 optimal weight: 0.7980 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.168662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130880 restraints weight = 25906.611| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.43 r_work: 0.3093 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18702 Z= 0.122 Angle : 0.493 8.971 25234 Z= 0.263 Chirality : 0.039 0.207 2826 Planarity : 0.003 0.045 3106 Dihedral : 3.962 41.522 2527 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.65 % Favored : 97.21 % Rotamer: Outliers : 2.76 % Allowed : 14.48 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: 1.88 (0.18), residues: 2298 helix: 3.11 (0.15), residues: 1280 sheet: -0.22 (0.43), residues: 144 loop : -1.51 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 675 TYR 0.014 0.001 TYR A 700 PHE 0.011 0.001 PHE B 546 TRP 0.011 0.001 TRP D 766 HIS 0.003 0.001 HIS G 59 Details of bonding type rmsd covalent geometry : bond 0.00273 (18690) covalent geometry : angle 0.49258 (25210) SS BOND : bond 0.00122 ( 12) SS BOND : angle 0.56455 ( 24) hydrogen bonds : bond 0.05595 ( 1047) hydrogen bonds : angle 3.58809 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 235 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: A 673 TYR cc_start: 0.8662 (t80) cc_final: 0.8355 (t80) REVERT: B 421 TYR cc_start: 0.7163 (m-80) cc_final: 0.6836 (m-80) REVERT: B 521 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8697 (mp) REVERT: B 769 ASP cc_start: 0.7979 (m-30) cc_final: 0.7568 (m-30) REVERT: C 498 LEU cc_start: 0.8127 (pt) cc_final: 0.7790 (pt) REVERT: C 657 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: C 673 TYR cc_start: 0.8463 (t80) cc_final: 0.8121 (t80) REVERT: D 402 GLU cc_start: 0.8567 (tp30) cc_final: 0.8178 (tp30) REVERT: D 439 LYS cc_start: 0.6859 (ptpt) cc_final: 0.6397 (mmmt) REVERT: D 638 ASP cc_start: 0.7334 (m-30) cc_final: 0.6446 (t0) REVERT: E 17 PHE cc_start: 0.8946 (t80) cc_final: 0.8648 (t80) REVERT: E 29 THR cc_start: 0.8111 (m) cc_final: 0.7821 (m) REVERT: E 36 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.7136 (mtp-110) REVERT: E 57 MET cc_start: 0.6608 (mmp) cc_final: 0.6345 (mmp) REVERT: E 73 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8624 (ttmm) REVERT: E 98 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7424 (mtt90) REVERT: E 202 ASP cc_start: 0.8387 (t70) cc_final: 0.8043 (t70) REVERT: F 58 THR cc_start: 0.8736 (p) cc_final: 0.8294 (t) REVERT: F 128 LYS cc_start: 0.7049 (mptt) cc_final: 0.6284 (tptt) REVERT: F 198 HIS cc_start: 0.7444 (t70) cc_final: 0.6894 (m-70) REVERT: G 11 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7003 (mt) REVERT: G 17 PHE cc_start: 0.8917 (t80) cc_final: 0.8547 (t80) REVERT: G 29 THR cc_start: 0.8098 (m) cc_final: 0.7813 (m) REVERT: G 36 ARG cc_start: 0.7359 (mmm-85) cc_final: 0.7037 (mmm-85) REVERT: G 173 TYR cc_start: 0.8913 (p90) cc_final: 0.7693 (p90) REVERT: G 202 ASP cc_start: 0.8015 (t70) cc_final: 0.7795 (t70) REVERT: H 58 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8154 (t) REVERT: H 94 GLU cc_start: 0.8073 (pm20) cc_final: 0.7744 (pt0) REVERT: H 130 ARG cc_start: 0.5968 (mtt180) cc_final: 0.5458 (mmm160) outliers start: 54 outliers final: 49 residues processed: 270 average time/residue: 0.1410 time to fit residues: 57.3850 Evaluate side-chains 287 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 421 TYR Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 150 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 217 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114685 restraints weight = 25942.846| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.20 r_work: 0.3056 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 18702 Z= 0.310 Angle : 0.689 9.063 25234 Z= 0.371 Chirality : 0.046 0.195 2826 Planarity : 0.005 0.055 3106 Dihedral : 4.838 52.581 2527 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.35 % Favored : 95.52 % Rotamer: Outliers : 2.86 % Allowed : 14.53 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.21 (0.18), residues: 2298 helix: 2.52 (0.14), residues: 1260 sheet: -0.68 (0.38), residues: 178 loop : -1.62 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 675 TYR 0.020 0.002 TYR C 732 PHE 0.028 0.003 PHE A 495 TRP 0.021 0.002 TRP B 578 HIS 0.014 0.002 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00762 (18690) covalent geometry : angle 0.68862 (25210) SS BOND : bond 0.00245 ( 12) SS BOND : angle 0.98601 ( 24) hydrogen bonds : bond 0.09961 ( 1047) hydrogen bonds : angle 4.41097 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 657 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: A 673 TYR cc_start: 0.8600 (t80) cc_final: 0.8277 (t80) REVERT: C 498 LEU cc_start: 0.8314 (pt) cc_final: 0.8014 (pt) REVERT: C 657 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: C 673 TYR cc_start: 0.8527 (t80) cc_final: 0.8160 (t80) REVERT: D 439 LYS cc_start: 0.7031 (ptpt) cc_final: 0.6515 (mmmt) REVERT: E 17 PHE cc_start: 0.9067 (t80) cc_final: 0.8755 (t80) REVERT: E 36 ARG cc_start: 0.7668 (mtp-110) cc_final: 0.7388 (mtp-110) REVERT: E 57 MET cc_start: 0.6933 (mmp) cc_final: 0.6612 (mmp) REVERT: E 202 ASP cc_start: 0.8516 (t70) cc_final: 0.8262 (t70) REVERT: F 127 TYR cc_start: 0.6556 (m-80) cc_final: 0.6339 (m-80) REVERT: F 128 LYS cc_start: 0.7380 (mptt) cc_final: 0.6673 (tptt) REVERT: F 134 ILE cc_start: 0.8247 (mm) cc_final: 0.8014 (mm) REVERT: F 202 ASP cc_start: 0.8063 (t0) cc_final: 0.7441 (m-30) REVERT: G 36 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7338 (mmm-85) REVERT: G 125 GLU cc_start: 0.8181 (tt0) cc_final: 0.7975 (tm-30) REVERT: G 202 ASP cc_start: 0.8330 (t70) cc_final: 0.8125 (t70) REVERT: H 94 GLU cc_start: 0.8242 (pm20) cc_final: 0.7793 (pt0) REVERT: H 130 ARG cc_start: 0.6256 (mtt180) cc_final: 0.5633 (mmm160) REVERT: H 202 ASP cc_start: 0.8061 (t0) cc_final: 0.7227 (m-30) outliers start: 56 outliers final: 48 residues processed: 280 average time/residue: 0.1243 time to fit residues: 52.3841 Evaluate side-chains 273 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 453 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 614 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 693 VAL Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 463 MET Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 543 VAL Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 VAL Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain C residue 659 PHE Chi-restraints excluded: chain C residue 795 VAL Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 614 SER Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 723 VAL Chi-restraints excluded: chain D residue 744 THR Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 67 CYS Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain H residue 65 THR Chi-restraints excluded: chain H residue 67 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 18 optimal weight: 0.8980 chunk 141 optimal weight: 0.0470 chunk 140 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 167 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 205 optimal weight: 0.7980 chunk 176 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 204 HIS ** H 204 HIS ** 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 = 0.3961 r_free = 0.3961 target = 0.166952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.129569 restraints weight = 25865.987| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.55 r_work: 0.3068 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18702 Z= 0.124 Angle : 0.514 9.217 25234 Z= 0.275 Chirality : 0.039 0.205 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.292 51.072 2527 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.61 % Favored : 97.26 % Rotamer: Outliers : 2.35 % Allowed : 15.09 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: 1.65 (0.18), residues: 2298 helix: 2.98 (0.15), residues: 1262 sheet: -0.59 (0.40), residues: 168 loop : -1.57 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 675 TYR 0.020 0.001 TYR A 700 PHE 0.010 0.001 PHE B 438 TRP 0.012 0.001 TRP G 177 HIS 0.008 0.001 HIS H 204 Details of bonding type rmsd covalent geometry : bond 0.00266 (18690) covalent geometry : angle 0.51395 (25210) SS BOND : bond 0.00109 ( 12) SS BOND : angle 0.63998 ( 24) hydrogen bonds : bond 0.05963 ( 1047) hydrogen bonds : angle 3.76279 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.08 seconds wall clock time: 69 minutes 53.78 seconds (4193.78 seconds total)