Starting phenix.real_space_refine on Mon Jun 16 05:55:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mrn_48560/06_2025/9mrn_48560.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mrn_48560/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mrn_48560/06_2025/9mrn_48560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mrn_48560/06_2025/9mrn_48560.map" model { file = "/net/cci-nas-00/data/ceres_data/9mrn_48560/06_2025/9mrn_48560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mrn_48560/06_2025/9mrn_48560.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.09, per 1000 atoms: 0.66 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: 4.95 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.91 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: 6.30 Time building geometry restraints manager: 5.84 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 819 or resid 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: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.490 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- 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 : 2.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (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 TRP 0.031 0.003 TRP F 177 HIS 0.005 0.001 HIS E 204 PHE 0.036 0.002 PHE A 574 TYR 0.036 0.003 TYR C 732 ARG 0.023 0.002 ARG B 661 Details of bonding type rmsd hydrogen bonds : bond 0.17378 ( 1047) hydrogen bonds : angle 6.06702 ( 3063) SS BOND : bond 0.00259 ( 12) SS BOND : angle 1.01018 ( 24) covalent geometry : bond 0.00529 (18690) covalent geometry : angle 0.77344 (25210) *********************** 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 : 1.960 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: 0.3921 time to fit residues: 255.7623 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 : 1.950 ------------------------------------------------------------------------------- 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 195 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4000 r_free = 0.4000 target = 0.170544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132758 restraints weight = 25829.194| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 4.71 r_work: 0.3117 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2361 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= 0.151 Angle : 0.590 8.188 25234 Z= 0.320 Chirality : 0.041 0.168 2826 Planarity : 0.004 0.056 3106 Dihedral : 5.383 60.857 2537 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.39 % Favored : 97.48 % Rotamer: Outliers : 1.94 % Allowed : 8.39 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2298 helix: 2.49 (0.14), residues: 1268 sheet: -0.03 (0.34), residues: 194 loop : -0.96 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 177 HIS 0.003 0.001 HIS E 131 PHE 0.017 0.002 PHE A 574 TYR 0.019 0.002 TYR F 127 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.06918 ( 1047) hydrogen bonds : angle 4.24167 ( 3063) SS BOND : bond 0.00333 ( 12) SS BOND : angle 0.75064 ( 24) covalent geometry : bond 0.00332 (18690) covalent geometry : angle 0.58938 (25210) *********************** 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 323 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 285 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7749 (mmt) cc_final: 0.7481 (mmt) REVERT: A 670 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8522 (mtm) REVERT: A 721 MET cc_start: 0.7497 (ttm) cc_final: 0.7099 (tpp) REVERT: B 414 MET cc_start: 0.5829 (mpp) cc_final: 0.5384 (ptp) REVERT: B 503 MET cc_start: 0.8549 (ttm) cc_final: 0.8177 (ttp) REVERT: C 414 MET cc_start: 0.7090 (mpp) cc_final: 0.6639 (ptp) REVERT: C 721 MET cc_start: 0.7523 (ttt) cc_final: 0.7300 (tpt) REVERT: D 594 ARG cc_start: 0.8645 (ptm160) cc_final: 0.8271 (ttp80) REVERT: E 17 PHE cc_start: 0.8899 (t80) cc_final: 0.8471 (t80) REVERT: E 29 THR cc_start: 0.8438 (m) cc_final: 0.8093 (m) REVERT: E 98 ARG cc_start: 0.7723 (mtt90) cc_final: 0.7381 (mtt90) REVERT: E 116 MET cc_start: 0.7996 (mmm) cc_final: 0.7744 (mtm) REVERT: E 202 ASP cc_start: 0.8238 (t70) cc_final: 0.7937 (t70) REVERT: F 94 GLU cc_start: 0.7975 (pm20) cc_final: 0.7506 (pt0) REVERT: F 125 GLU cc_start: 0.7465 (tp30) cc_final: 0.7208 (tp30) REVERT: F 128 LYS cc_start: 0.7327 (mptt) cc_final: 0.6682 (tptt) REVERT: F 202 ASP cc_start: 0.8051 (t70) cc_final: 0.7314 (m-30) REVERT: G 17 PHE cc_start: 0.8886 (t80) cc_final: 0.8445 (t80) REVERT: G 29 THR cc_start: 0.8383 (m) cc_final: 0.8082 (m) REVERT: G 116 MET cc_start: 0.8089 (mmm) cc_final: 0.7767 (mtm) REVERT: G 173 TYR cc_start: 0.8837 (p90) cc_final: 0.7555 (p90) REVERT: G 202 ASP cc_start: 0.8061 (t70) cc_final: 0.7786 (t70) REVERT: H 130 ARG cc_start: 0.6164 (mtt180) cc_final: 0.5662 (mmm160) outliers start: 38 outliers final: 23 residues processed: 309 average time/residue: 0.3663 time to fit residues: 161.2139 Evaluate side-chains 260 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 670 MET 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 590 ASP Chi-restraints excluded: chain C residue 626 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 180 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 187 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 188 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.169989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131121 restraints weight = 25649.725| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.36 r_work: 0.3121 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2869 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= 0.136 Angle : 0.532 8.611 25234 Z= 0.286 Chirality : 0.040 0.161 2826 Planarity : 0.004 0.045 3106 Dihedral : 4.731 54.236 2529 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % Rotamer: Outliers : 2.40 % Allowed : 10.28 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2298 helix: 2.88 (0.15), residues: 1272 sheet: 0.06 (0.35), residues: 194 loop : -1.03 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 177 HIS 0.020 0.001 HIS F 204 PHE 0.013 0.001 PHE A 574 TYR 0.015 0.001 TYR D 405 ARG 0.007 0.000 ARG C 675 Details of bonding type rmsd hydrogen bonds : bond 0.06337 ( 1047) hydrogen bonds : angle 3.94197 ( 3063) SS BOND : bond 0.00232 ( 12) SS BOND : angle 0.69515 ( 24) covalent geometry : bond 0.00295 (18690) covalent geometry : angle 0.53181 (25210) *********************** 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 300 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 253 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 670 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8585 (mtm) REVERT: A 700 TYR cc_start: 0.5583 (t80) cc_final: 0.5368 (t80) REVERT: A 721 MET cc_start: 0.7475 (ttm) cc_final: 0.7067 (tpp) REVERT: B 414 MET cc_start: 0.5822 (mpp) cc_final: 0.5507 (ptp) REVERT: B 453 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6850 (ptm160) REVERT: B 628 ARG cc_start: 0.8851 (ppt170) cc_final: 0.8567 (ppt170) REVERT: C 673 TYR cc_start: 0.8597 (t80) cc_final: 0.8239 (t80) REVERT: C 708 MET cc_start: 0.8525 (mmt) cc_final: 0.7746 (mtt) REVERT: C 721 MET cc_start: 0.7527 (ttt) cc_final: 0.7319 (tpt) REVERT: D 405 TYR cc_start: 0.8743 (m-10) cc_final: 0.8514 (m-80) REVERT: D 594 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8259 (ttp80) REVERT: D 756 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: E 17 PHE cc_start: 0.8898 (t80) cc_final: 0.8464 (t80) REVERT: E 29 THR cc_start: 0.8142 (m) cc_final: 0.7850 (m) REVERT: E 36 ARG cc_start: 0.7022 (mtp-110) cc_final: 0.6715 (mtp-110) REVERT: E 57 MET cc_start: 0.6485 (mmp) cc_final: 0.5992 (mmp) REVERT: E 202 ASP cc_start: 0.8369 (t70) cc_final: 0.8047 (t70) REVERT: F 36 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7449 (mtm-85) REVERT: F 58 THR cc_start: 0.8753 (p) cc_final: 0.8299 (t) REVERT: F 94 GLU cc_start: 0.8082 (pm20) cc_final: 0.7724 (pt0) REVERT: F 202 ASP cc_start: 0.8001 (t70) cc_final: 0.7761 (t0) REVERT: G 11 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6962 (mt) REVERT: G 17 PHE cc_start: 0.8921 (t80) cc_final: 0.8478 (t80) REVERT: G 29 THR cc_start: 0.8141 (m) cc_final: 0.7842 (m) REVERT: G 36 ARG cc_start: 0.7394 (mmm-85) cc_final: 0.7076 (mmm-85) REVERT: G 116 MET cc_start: 0.8066 (mmm) cc_final: 0.7837 (mtt) REVERT: G 125 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 173 TYR cc_start: 0.8832 (p90) cc_final: 0.7604 (p90) REVERT: G 202 ASP cc_start: 0.7985 (t70) cc_final: 0.7727 (t70) REVERT: H 58 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8193 (t) REVERT: H 94 GLU cc_start: 0.8172 (pm20) cc_final: 0.7540 (pt0) REVERT: H 130 ARG cc_start: 0.6135 (mtt180) cc_final: 0.5678 (mmm160) outliers start: 47 outliers final: 34 residues processed: 278 average time/residue: 0.3431 time to fit residues: 139.2844 Evaluate side-chains 265 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 670 MET Chi-restraints excluded: chain A residue 716 LYS Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 453 ARG 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 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 614 SER 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 30 ASP 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 58 THR 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 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.0470 chunk 227 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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 = 0.168031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129031 restraints weight = 25761.663| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.38 r_work: 0.3097 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18702 Z= 0.143 Angle : 0.520 8.526 25234 Z= 0.281 Chirality : 0.040 0.156 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.506 47.759 2529 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.44 % Favored : 97.43 % Rotamer: Outliers : 3.12 % Allowed : 10.49 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2298 helix: 2.88 (0.15), residues: 1282 sheet: -0.08 (0.39), residues: 150 loop : -1.23 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 177 HIS 0.004 0.001 HIS G 59 PHE 0.016 0.001 PHE D 546 TYR 0.014 0.001 TYR D 405 ARG 0.005 0.000 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.06600 ( 1047) hydrogen bonds : angle 3.85650 ( 3063) SS BOND : bond 0.00273 ( 12) SS BOND : angle 0.69385 ( 24) covalent geometry : bond 0.00322 (18690) covalent geometry : angle 0.52002 (25210) *********************** 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 303 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 242 time to evaluate : 2.144 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8484 (pp) REVERT: A 657 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6131 (mp0) REVERT: A 670 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8615 (mtm) REVERT: A 673 TYR cc_start: 0.8637 (t80) cc_final: 0.8330 (t80) REVERT: A 721 MET cc_start: 0.7518 (ttm) cc_final: 0.7100 (tpp) REVERT: B 628 ARG cc_start: 0.8936 (ppt170) cc_final: 0.8727 (ppt170) REVERT: C 657 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: C 673 TYR cc_start: 0.8552 (t80) cc_final: 0.8160 (t80) REVERT: C 708 MET cc_start: 0.8561 (mmt) cc_final: 0.7741 (mtt) REVERT: D 405 TYR cc_start: 0.8772 (m-80) cc_final: 0.8546 (m-80) REVERT: D 421 TYR cc_start: 0.7194 (m-80) cc_final: 0.6798 (m-80) REVERT: D 439 LYS cc_start: 0.7081 (ptpt) cc_final: 0.6643 (mmmt) REVERT: D 594 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8292 (ttp80) REVERT: E 17 PHE cc_start: 0.8883 (t80) cc_final: 0.8480 (t80) REVERT: E 29 THR cc_start: 0.8226 (m) cc_final: 0.7931 (m) REVERT: E 36 ARG cc_start: 0.7140 (mtp-110) cc_final: 0.6763 (mtp-110) REVERT: E 98 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7517 (mtt90) REVERT: E 202 ASP cc_start: 0.8401 (t70) cc_final: 0.8080 (t70) REVERT: F 36 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: F 58 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8260 (t) REVERT: F 94 GLU cc_start: 0.8100 (pm20) cc_final: 0.7788 (pt0) REVERT: F 202 ASP cc_start: 0.7980 (t70) cc_final: 0.7771 (t0) REVERT: G 11 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7052 (mt) REVERT: G 17 PHE cc_start: 0.8910 (t80) cc_final: 0.8494 (t80) REVERT: G 29 THR cc_start: 0.8175 (m) cc_final: 0.7875 (m) REVERT: G 36 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.7032 (mmm-85) REVERT: G 125 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7858 (tm-30) REVERT: G 173 TYR cc_start: 0.8805 (p90) cc_final: 0.7671 (p90) REVERT: G 202 ASP cc_start: 0.8016 (t70) cc_final: 0.7749 (t0) REVERT: H 58 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8211 (t) REVERT: H 94 GLU cc_start: 0.8157 (pm20) cc_final: 0.7617 (pt0) REVERT: H 130 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5605 (mmm160) outliers start: 61 outliers final: 45 residues processed: 281 average time/residue: 0.3553 time to fit residues: 145.2834 Evaluate side-chains 282 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 2.104 ------------------------------------------------------------------------------- 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 659 PHE Chi-restraints excluded: chain A residue 670 MET 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 503 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 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 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 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 58 THR 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 30 ASP 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.166287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128761 restraints weight = 25875.000| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 4.59 r_work: 0.3039 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18702 Z= 0.160 Angle : 0.533 8.912 25234 Z= 0.287 Chirality : 0.040 0.237 2826 Planarity : 0.004 0.049 3106 Dihedral : 4.442 42.071 2529 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.00 % Favored : 96.87 % Rotamer: Outliers : 3.48 % Allowed : 11.46 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.18), residues: 2298 helix: 2.88 (0.15), residues: 1280 sheet: -0.21 (0.41), residues: 138 loop : -1.31 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 177 HIS 0.008 0.001 HIS F 204 PHE 0.014 0.001 PHE A 495 TYR 0.015 0.001 TYR C 424 ARG 0.003 0.000 ARG B 675 Details of bonding type rmsd hydrogen bonds : bond 0.07054 ( 1047) hydrogen bonds : angle 3.88401 ( 3063) SS BOND : bond 0.00143 ( 12) SS BOND : angle 0.65804 ( 24) covalent geometry : bond 0.00373 (18690) covalent geometry : angle 0.53306 (25210) *********************** 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 306 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 238 time to evaluate : 1.995 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8506 (pp) REVERT: A 657 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 673 TYR cc_start: 0.8628 (t80) cc_final: 0.8334 (t80) REVERT: A 721 MET cc_start: 0.7527 (ttm) cc_final: 0.7290 (tpp) REVERT: B 405 TYR cc_start: 0.8800 (m-80) cc_final: 0.8594 (m-80) REVERT: B 521 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8734 (mp) REVERT: C 657 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: C 673 TYR cc_start: 0.8518 (t80) cc_final: 0.8126 (t80) REVERT: D 405 TYR cc_start: 0.8841 (m-80) cc_final: 0.8594 (m-80) REVERT: D 421 TYR cc_start: 0.7214 (m-80) cc_final: 0.6837 (m-80) REVERT: D 594 ARG cc_start: 0.8798 (ptm160) cc_final: 0.8366 (ttp80) REVERT: D 756 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: E 17 PHE cc_start: 0.8912 (t80) cc_final: 0.8552 (t80) REVERT: E 29 THR cc_start: 0.8353 (m) cc_final: 0.8033 (m) REVERT: E 36 ARG cc_start: 0.7233 (mtp-110) cc_final: 0.6897 (mtp-110) REVERT: E 57 MET cc_start: 0.6683 (mmp) cc_final: 0.6231 (mmp) REVERT: E 98 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7442 (mtt90) REVERT: E 202 ASP cc_start: 0.8495 (t70) cc_final: 0.8128 (t70) REVERT: F 58 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8369 (t) REVERT: F 94 GLU cc_start: 0.8096 (pm20) cc_final: 0.7834 (pt0) REVERT: F 128 LYS cc_start: 0.7197 (mptt) cc_final: 0.6548 (tptt) REVERT: F 202 ASP cc_start: 0.8149 (t70) cc_final: 0.7490 (m-30) REVERT: G 11 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7040 (mt) REVERT: G 17 PHE cc_start: 0.8942 (t80) cc_final: 0.8537 (t80) REVERT: G 29 THR cc_start: 0.8361 (m) cc_final: 0.8035 (m) REVERT: G 98 ARG cc_start: 0.7767 (mtt90) cc_final: 0.7462 (mtt90) REVERT: G 125 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7816 (tm-30) REVERT: G 202 ASP cc_start: 0.8063 (t70) cc_final: 0.7810 (t0) REVERT: H 58 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8230 (t) REVERT: H 94 GLU cc_start: 0.8199 (pm20) cc_final: 0.7674 (pt0) REVERT: H 130 ARG cc_start: 0.6145 (mtt180) cc_final: 0.5602 (mmm160) outliers start: 68 outliers final: 49 residues processed: 282 average time/residue: 0.3271 time to fit residues: 135.3530 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 : 2.041 ------------------------------------------------------------------------------- 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 659 PHE Chi-restraints excluded: chain A residue 683 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 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 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 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 C residue 817 LYS 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 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 119 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 58 THR 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 24 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.0020 chunk 52 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 177 optimal weight: 0.0770 chunk 126 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5946 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.168354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130594 restraints weight = 25949.384| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 4.32 r_work: 0.3087 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18702 Z= 0.126 Angle : 0.499 8.595 25234 Z= 0.268 Chirality : 0.039 0.191 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.174 36.870 2527 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.61 % Rotamer: Outliers : 3.27 % Allowed : 12.02 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.18), residues: 2298 helix: 3.00 (0.15), residues: 1284 sheet: -0.23 (0.42), residues: 136 loop : -1.28 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 177 HIS 0.006 0.001 HIS F 204 PHE 0.019 0.001 PHE D 546 TYR 0.012 0.001 TYR C 424 ARG 0.005 0.000 ARG F 130 Details of bonding type rmsd hydrogen bonds : bond 0.06042 ( 1047) hydrogen bonds : angle 3.70361 ( 3063) SS BOND : bond 0.00154 ( 12) SS BOND : angle 0.64576 ( 24) covalent geometry : bond 0.00276 (18690) covalent geometry : angle 0.49885 (25210) *********************** 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 303 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 239 time to evaluate : 2.096 Fit side-chains REVERT: A 498 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (pp) REVERT: A 657 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: A 673 TYR cc_start: 0.8588 (t80) cc_final: 0.8276 (t80) REVERT: A 721 MET cc_start: 0.7532 (ttm) cc_final: 0.7170 (tpp) REVERT: B 421 TYR cc_start: 0.7174 (m-80) cc_final: 0.6882 (m-80) REVERT: B 521 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 657 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: C 673 TYR cc_start: 0.8497 (t80) cc_final: 0.8100 (t80) REVERT: D 402 GLU cc_start: 0.8541 (tp30) cc_final: 0.8192 (tp30) REVERT: D 405 TYR cc_start: 0.8852 (m-80) cc_final: 0.8630 (m-80) REVERT: D 421 TYR cc_start: 0.7274 (m-80) cc_final: 0.7001 (m-80) REVERT: D 756 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: E 11 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6942 (mt) REVERT: E 17 PHE cc_start: 0.8928 (t80) cc_final: 0.8567 (t80) REVERT: E 29 THR cc_start: 0.8205 (m) cc_final: 0.7904 (m) REVERT: E 36 ARG cc_start: 0.7343 (mtp-110) cc_final: 0.7013 (mtp-110) REVERT: E 57 MET cc_start: 0.6648 (mmp) cc_final: 0.6176 (mmp) REVERT: E 98 ARG cc_start: 0.7752 (mtt90) cc_final: 0.7431 (mtt90) REVERT: E 202 ASP cc_start: 0.8452 (t70) cc_final: 0.8118 (t70) REVERT: F 36 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: F 58 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8312 (t) REVERT: F 94 GLU cc_start: 0.8099 (pm20) cc_final: 0.7874 (pt0) REVERT: F 128 LYS cc_start: 0.7135 (mptt) cc_final: 0.6476 (tptt) REVERT: F 202 ASP cc_start: 0.8107 (t70) cc_final: 0.7887 (t0) REVERT: G 11 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7136 (mt) REVERT: G 17 PHE cc_start: 0.8950 (t80) cc_final: 0.8543 (t80) REVERT: G 29 THR cc_start: 0.8203 (m) cc_final: 0.7908 (m) REVERT: G 125 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7910 (tm-30) REVERT: G 173 TYR cc_start: 0.8890 (p90) cc_final: 0.7763 (p90) REVERT: G 202 ASP cc_start: 0.7988 (t70) cc_final: 0.7739 (t0) REVERT: H 58 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8223 (t) REVERT: H 94 GLU cc_start: 0.8123 (pm20) cc_final: 0.7597 (pt0) REVERT: H 130 ARG cc_start: 0.6081 (mtt180) cc_final: 0.5601 (mmm160) outliers start: 64 outliers final: 45 residues processed: 284 average time/residue: 0.3073 time to fit residues: 130.8876 Evaluate side-chains 285 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 659 PHE 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 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 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 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 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 E residue 121 ILE Chi-restraints excluded: chain F residue 58 THR 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 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 171 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 198 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121198 restraints weight = 25772.043| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.30 r_work: 0.3113 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18702 Z= 0.203 Angle : 0.576 8.955 25234 Z= 0.311 Chirality : 0.042 0.173 2826 Planarity : 0.004 0.052 3106 Dihedral : 4.464 38.703 2527 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 3.43 % Allowed : 12.33 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 2298 helix: 2.74 (0.15), residues: 1280 sheet: -0.22 (0.40), residues: 158 loop : -1.50 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 578 HIS 0.014 0.001 HIS F 204 PHE 0.019 0.002 PHE A 495 TYR 0.019 0.002 TYR C 424 ARG 0.008 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.08195 ( 1047) hydrogen bonds : angle 4.06543 ( 3063) SS BOND : bond 0.00182 ( 12) SS BOND : angle 0.75555 ( 24) covalent geometry : bond 0.00489 (18690) covalent geometry : angle 0.57628 (25210) *********************** 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 311 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 244 time to evaluate : 1.977 Fit side-chains REVERT: A 498 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (pp) REVERT: A 657 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: A 673 TYR cc_start: 0.8581 (t80) cc_final: 0.8304 (t80) REVERT: B 453 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7147 (ptm160) REVERT: C 498 LEU cc_start: 0.8155 (pt) cc_final: 0.7835 (pt) REVERT: C 657 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: C 673 TYR cc_start: 0.8486 (t80) cc_final: 0.8123 (t80) REVERT: D 405 TYR cc_start: 0.8871 (m-80) cc_final: 0.8656 (m-80) REVERT: E 36 ARG cc_start: 0.7447 (mtp-110) cc_final: 0.7163 (mtp-110) REVERT: E 202 ASP cc_start: 0.8376 (t70) cc_final: 0.8098 (t70) REVERT: F 58 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8404 (t) REVERT: F 128 LYS cc_start: 0.7030 (mptt) cc_final: 0.6410 (tptt) REVERT: F 202 ASP cc_start: 0.8148 (t70) cc_final: 0.7574 (m-30) REVERT: G 36 ARG cc_start: 0.7377 (mmm-85) cc_final: 0.7006 (mmm160) REVERT: G 40 LYS cc_start: 0.6443 (tttm) cc_final: 0.6210 (ttpt) REVERT: G 98 ARG cc_start: 0.7704 (mtt90) cc_final: 0.7480 (mtt90) REVERT: G 125 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7725 (tm-30) REVERT: G 202 ASP cc_start: 0.8085 (t70) cc_final: 0.7881 (t70) REVERT: H 58 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8323 (t) REVERT: H 94 GLU cc_start: 0.8106 (pm20) cc_final: 0.7597 (pt0) REVERT: H 116 MET cc_start: 0.8850 (mmm) cc_final: 0.8622 (mtt) REVERT: H 130 ARG cc_start: 0.6160 (mtt180) cc_final: 0.5670 (mmm160) REVERT: H 202 ASP cc_start: 0.7880 (t0) cc_final: 0.7087 (m-30) outliers start: 67 outliers final: 54 residues processed: 289 average time/residue: 0.3243 time to fit residues: 139.0651 Evaluate side-chains 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 1.939 ------------------------------------------------------------------------------- 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 659 PHE 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 395 VAL Chi-restraints excluded: chain B residue 398 THR 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 750 VAL Chi-restraints excluded: chain C residue 399 THR 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 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 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 723 VAL Chi-restraints excluded: chain D residue 744 THR 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 D residue 795 VAL 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 58 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 128 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 chunk 230 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 171 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131352 restraints weight = 25873.783| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 4.68 r_work: 0.3083 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3761 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= 0.123 Angle : 0.505 9.341 25234 Z= 0.270 Chirality : 0.039 0.193 2826 Planarity : 0.004 0.044 3106 Dihedral : 4.141 38.459 2527 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.13 % Favored : 97.74 % Rotamer: Outliers : 3.07 % Allowed : 13.40 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2298 helix: 3.02 (0.15), residues: 1276 sheet: -0.31 (0.39), residues: 168 loop : -1.43 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 766 HIS 0.011 0.001 HIS F 204 PHE 0.011 0.001 PHE B 546 TYR 0.013 0.001 TYR C 700 ARG 0.007 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.05879 ( 1047) hydrogen bonds : angle 3.68521 ( 3063) SS BOND : bond 0.00131 ( 12) SS BOND : angle 0.58696 ( 24) covalent geometry : bond 0.00264 (18690) covalent geometry : angle 0.50509 (25210) *********************** 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 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 2.238 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8328 (pp) REVERT: A 657 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6106 (mp0) REVERT: A 673 TYR cc_start: 0.8608 (t80) cc_final: 0.8299 (t80) REVERT: B 521 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8738 (mp) REVERT: C 498 LEU cc_start: 0.8085 (pt) cc_final: 0.7733 (pt) REVERT: C 657 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: C 673 TYR cc_start: 0.8475 (t80) cc_final: 0.8125 (t80) REVERT: D 402 GLU cc_start: 0.8556 (tp30) cc_final: 0.8157 (tp30) REVERT: D 421 TYR cc_start: 0.7049 (m-80) cc_final: 0.6792 (m-80) REVERT: D 439 LYS cc_start: 0.7017 (ptpt) cc_final: 0.6593 (mmtm) REVERT: D 638 ASP cc_start: 0.7401 (m-30) cc_final: 0.6470 (t0) REVERT: D 756 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: E 11 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6849 (mt) REVERT: E 17 PHE cc_start: 0.8906 (t80) cc_final: 0.8626 (t80) REVERT: E 29 THR cc_start: 0.8364 (m) cc_final: 0.8084 (m) REVERT: E 36 ARG cc_start: 0.7466 (mtp-110) cc_final: 0.7140 (mtp-110) REVERT: E 57 MET cc_start: 0.6644 (mmp) cc_final: 0.6241 (mmp) REVERT: E 98 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7430 (mtt90) REVERT: E 202 ASP cc_start: 0.8417 (t70) cc_final: 0.8100 (t70) REVERT: F 58 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8304 (t) REVERT: F 128 LYS cc_start: 0.7106 (mptt) cc_final: 0.6413 (tptt) REVERT: F 202 ASP cc_start: 0.8121 (t70) cc_final: 0.7910 (t0) REVERT: G 11 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7025 (mt) REVERT: G 17 PHE cc_start: 0.8926 (t80) cc_final: 0.8653 (t80) REVERT: G 29 THR cc_start: 0.8354 (m) cc_final: 0.8082 (m) REVERT: G 36 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6855 (mmm160) REVERT: G 40 LYS cc_start: 0.6159 (tttm) cc_final: 0.5950 (ttpt) REVERT: G 75 LEU cc_start: 0.8573 (mt) cc_final: 0.8270 (pp) REVERT: G 125 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7889 (tm-30) REVERT: G 202 ASP cc_start: 0.8070 (t70) cc_final: 0.7801 (t0) REVERT: H 58 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8203 (t) REVERT: H 94 GLU cc_start: 0.8113 (pm20) cc_final: 0.7752 (pt0) REVERT: H 130 ARG cc_start: 0.6103 (mtt180) cc_final: 0.5531 (mmm160) outliers start: 60 outliers final: 47 residues processed: 278 average time/residue: 0.3150 time to fit residues: 132.1021 Evaluate side-chains 288 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 232 time to evaluate : 2.070 ------------------------------------------------------------------------------- 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 502 ILE 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 398 THR 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 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 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 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 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 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 795 VAL 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 E residue 121 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 58 THR 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 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 184 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 163 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.166337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123995 restraints weight = 26064.237| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.25 r_work: 0.3199 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3799 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= 0.145 Angle : 0.519 8.603 25234 Z= 0.277 Chirality : 0.039 0.170 2826 Planarity : 0.004 0.047 3106 Dihedral : 4.139 39.169 2527 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 3.22 % Allowed : 13.40 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.18), residues: 2298 helix: 2.98 (0.15), residues: 1276 sheet: -0.39 (0.39), residues: 168 loop : -1.48 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 766 HIS 0.006 0.001 HIS F 204 PHE 0.013 0.001 PHE A 495 TYR 0.021 0.001 TYR D 405 ARG 0.006 0.000 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.06515 ( 1047) hydrogen bonds : angle 3.76349 ( 3063) SS BOND : bond 0.00125 ( 12) SS BOND : angle 0.61168 ( 24) covalent geometry : bond 0.00332 (18690) covalent geometry : angle 0.51893 (25210) *********************** 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 296 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 233 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8348 (pp) REVERT: A 657 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: A 673 TYR cc_start: 0.8597 (t80) cc_final: 0.8313 (t80) REVERT: B 521 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8796 (mp) REVERT: C 498 LEU cc_start: 0.8093 (pt) cc_final: 0.7752 (pt) REVERT: C 657 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: C 673 TYR cc_start: 0.8472 (t80) cc_final: 0.8133 (t80) REVERT: D 402 GLU cc_start: 0.8538 (tp30) cc_final: 0.8144 (tp30) REVERT: D 439 LYS cc_start: 0.6986 (ptpt) cc_final: 0.6559 (mmtm) REVERT: D 638 ASP cc_start: 0.7409 (m-30) cc_final: 0.6526 (t0) REVERT: D 756 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: E 17 PHE cc_start: 0.8933 (t80) cc_final: 0.8656 (t80) REVERT: E 36 ARG cc_start: 0.7522 (mtp-110) cc_final: 0.7130 (mtp-110) REVERT: E 57 MET cc_start: 0.6846 (mmp) cc_final: 0.6485 (mmp) REVERT: E 202 ASP cc_start: 0.8411 (t70) cc_final: 0.8098 (t70) REVERT: F 58 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8394 (t) REVERT: F 128 LYS cc_start: 0.7149 (mptt) cc_final: 0.6438 (tptt) REVERT: F 202 ASP cc_start: 0.8090 (t70) cc_final: 0.7878 (t0) REVERT: G 11 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7052 (mt) REVERT: G 17 PHE cc_start: 0.8963 (t80) cc_final: 0.8697 (t80) REVERT: G 29 THR cc_start: 0.8437 (m) cc_final: 0.8146 (m) REVERT: G 36 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6914 (mmm160) REVERT: G 40 LYS cc_start: 0.6370 (tttm) cc_final: 0.6161 (ttpt) REVERT: G 75 LEU cc_start: 0.8640 (mt) cc_final: 0.8369 (pp) REVERT: G 98 ARG cc_start: 0.7730 (mtt90) cc_final: 0.7525 (mtt90) REVERT: G 125 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 202 ASP cc_start: 0.8030 (t70) cc_final: 0.7763 (t0) REVERT: H 58 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8272 (t) REVERT: H 94 GLU cc_start: 0.8097 (pm20) cc_final: 0.7748 (pt0) REVERT: H 116 MET cc_start: 0.8785 (mmm) cc_final: 0.8494 (mtt) REVERT: H 130 ARG cc_start: 0.6099 (mtt180) cc_final: 0.5578 (mmm160) outliers start: 63 outliers final: 53 residues processed: 275 average time/residue: 0.3118 time to fit residues: 128.8892 Evaluate side-chains 294 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 502 ILE 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 398 THR 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 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 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 C residue 723 VAL 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 756 GLN Chi-restraints excluded: chain D residue 760 ASP Chi-restraints excluded: chain D residue 795 VAL 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 E residue 121 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 58 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 138 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 F 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125232 restraints weight = 25829.352| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.23 r_work: 0.3234 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3877 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= 0.123 Angle : 0.502 9.065 25234 Z= 0.267 Chirality : 0.039 0.166 2826 Planarity : 0.003 0.044 3106 Dihedral : 4.032 39.232 2527 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.35 % Favored : 97.52 % Rotamer: Outliers : 2.92 % Allowed : 13.81 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.18), residues: 2298 helix: 3.07 (0.15), residues: 1276 sheet: -0.41 (0.39), residues: 168 loop : -1.45 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 177 HIS 0.010 0.001 HIS F 204 PHE 0.012 0.001 PHE B 546 TYR 0.018 0.001 TYR D 405 ARG 0.006 0.000 ARG A 675 Details of bonding type rmsd hydrogen bonds : bond 0.05816 ( 1047) hydrogen bonds : angle 3.64847 ( 3063) SS BOND : bond 0.00118 ( 12) SS BOND : angle 0.58843 ( 24) covalent geometry : bond 0.00268 (18690) covalent geometry : angle 0.50210 (25210) ********************** 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 291 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 2.208 Fit side-chains revert: symmetry clash REVERT: A 498 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 657 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6136 (mp0) REVERT: A 673 TYR cc_start: 0.8582 (t80) cc_final: 0.8281 (t80) REVERT: B 521 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8765 (mp) REVERT: C 498 LEU cc_start: 0.8117 (pt) cc_final: 0.7772 (pt) REVERT: C 657 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: C 673 TYR cc_start: 0.8459 (t80) cc_final: 0.8113 (t80) REVERT: D 402 GLU cc_start: 0.8524 (tp30) cc_final: 0.8134 (tp30) REVERT: D 439 LYS cc_start: 0.6905 (ptpt) cc_final: 0.6445 (mmmt) REVERT: D 638 ASP cc_start: 0.7313 (m-30) cc_final: 0.6450 (t0) REVERT: E 11 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6853 (mt) REVERT: E 17 PHE cc_start: 0.8920 (t80) cc_final: 0.8638 (t80) REVERT: E 29 THR cc_start: 0.8304 (m) cc_final: 0.8032 (m) REVERT: E 36 ARG cc_start: 0.7389 (mtp-110) cc_final: 0.7146 (mtp-110) REVERT: E 57 MET cc_start: 0.6805 (mmp) cc_final: 0.6487 (mmp) REVERT: E 202 ASP cc_start: 0.8416 (t70) cc_final: 0.8090 (t70) REVERT: F 58 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8314 (t) REVERT: F 128 LYS cc_start: 0.7135 (mptt) cc_final: 0.6432 (tptt) REVERT: F 202 ASP cc_start: 0.8098 (t70) cc_final: 0.7882 (t0) REVERT: G 11 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7030 (mt) REVERT: G 17 PHE cc_start: 0.8942 (t80) cc_final: 0.8642 (t80) REVERT: G 29 THR cc_start: 0.8320 (m) cc_final: 0.8055 (m) REVERT: G 40 LYS cc_start: 0.6366 (tttm) cc_final: 0.6165 (ttpt) REVERT: G 75 LEU cc_start: 0.8639 (mt) cc_final: 0.8427 (pp) REVERT: G 125 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7839 (tm-30) REVERT: G 202 ASP cc_start: 0.8022 (t70) cc_final: 0.7753 (t0) REVERT: H 58 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8190 (t) REVERT: H 94 GLU cc_start: 0.8102 (pm20) cc_final: 0.7755 (pt0) REVERT: H 130 ARG cc_start: 0.6037 (mtt180) cc_final: 0.5505 (mmm160) outliers start: 57 outliers final: 48 residues processed: 273 average time/residue: 0.3587 time to fit residues: 148.5139 Evaluate side-chains 284 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 2.054 ------------------------------------------------------------------------------- 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 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 398 THR 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 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 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 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 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 D residue 795 VAL 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 E residue 121 ILE Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain F residue 58 THR 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 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 225 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3894 r_free = 0.3894 target = 0.160807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 128)---------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116368 restraints weight = 25764.222| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.20 r_work: 0.3080 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18702 Z= 0.258 Angle : 0.641 9.245 25234 Z= 0.344 Chirality : 0.044 0.181 2826 Planarity : 0.004 0.052 3106 Dihedral : 4.641 46.911 2527 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 3.43 % Allowed : 13.35 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.18), residues: 2298 helix: 2.63 (0.14), residues: 1260 sheet: -0.76 (0.39), residues: 178 loop : -1.56 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 578 HIS 0.012 0.002 HIS F 204 PHE 0.025 0.002 PHE A 495 TYR 0.025 0.002 TYR D 405 ARG 0.007 0.001 ARG G 36 Details of bonding type rmsd hydrogen bonds : bond 0.09215 ( 1047) hydrogen bonds : angle 4.29409 ( 3063) SS BOND : bond 0.00177 ( 12) SS BOND : angle 0.84639 ( 24) covalent geometry : bond 0.00628 (18690) covalent geometry : angle 0.64056 (25210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9584.63 seconds wall clock time: 165 minutes 46.73 seconds (9946.73 seconds total)