Starting phenix.real_space_refine on Thu Aug 6 11:14:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.cif Found real_map, /net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.map" model { file = "/net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/30yy_58158/08_2026/30yy_58158.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.044 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 12 5.16 5 C 9288 2.51 5 N 2280 2.21 5 O 2922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14502 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2418 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "A" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2412 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2418 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2418 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "D" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2418 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Chain: "E" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2418 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 289} Chain breaks: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.19 Number of scatterers: 14502 At special positions: 0 Unit cell: (201.36, 181.224, 73.832, 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 12 16.00 O 2922 8.00 N 2280 7.00 C 9288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.79 Conformation dependent library (CDL) restraints added in 585.8 milliseconds 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3432 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 8.6% alpha, 55.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'F' and resid 66 through 68 No H-bonds generated for 'chain 'F' and resid 66 through 68' Processing helix chain 'F' and resid 69 through 82 Processing helix chain 'F' and resid 599 through 603 removed outlier: 3.958A pdb=" N GLN F 603 " --> pdb=" O PRO F 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 621 Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 599 through 603 removed outlier: 4.070A pdb=" N GLN A 603 " --> pdb=" O PRO A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 621 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.989A pdb=" N GLN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 621 Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.888A pdb=" N GLN C 603 " --> pdb=" O PRO C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 621 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.867A pdb=" N GLN D 603 " --> pdb=" O PRO D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 621 Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.918A pdb=" N GLN E 603 " --> pdb=" O PRO E 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 621 Processing sheet with id=AA1, first strand: chain 'F' and resid 11 through 13 removed outlier: 7.051A pdb=" N ILE F 127 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 106 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA F 125 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU F 122 " --> pdb=" O PHE F 63 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLN F 58 " --> pdb=" O PRO F 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 13 removed outlier: 21.657A pdb=" N TYR F 98 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 18.266A pdb=" N ALA B 37 " --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 16.288A pdb=" N LYS F 100 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 13.040A pdb=" N TYR B 35 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N ASN F 102 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N ASN B 33 " --> pdb=" O ASN F 102 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN F 104 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS B 46 " --> pdb=" O THR B 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N SER B 36 " --> pdb=" O LYS B 44 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS B 44 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR B 38 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 41 through 49 removed outlier: 4.805A pdb=" N PHE F 42 " --> pdb=" O TYR F 38 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR F 38 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS F 44 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER F 36 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS F 46 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN D 104 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN F 33 " --> pdb=" O ASN D 102 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N ASN D 102 " --> pdb=" O ASN F 33 " (cutoff:3.500A) removed outlier: 13.136A pdb=" N TYR F 35 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 16.397A pdb=" N LYS D 100 " --> pdb=" O TYR F 35 " (cutoff:3.500A) removed outlier: 18.354A pdb=" N ALA F 37 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 21.738A pdb=" N TYR D 98 " --> pdb=" O ALA F 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 41 through 49 removed outlier: 4.805A pdb=" N PHE F 42 " --> pdb=" O TYR F 38 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TYR F 38 " --> pdb=" O PHE F 42 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS F 44 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER F 36 " --> pdb=" O LYS F 44 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS F 46 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLN D 104 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N ASN F 33 " --> pdb=" O ASN D 102 " (cutoff:3.500A) removed outlier: 10.468A pdb=" N ASN D 102 " --> pdb=" O ASN F 33 " (cutoff:3.500A) removed outlier: 13.136A pdb=" N TYR F 35 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 16.397A pdb=" N LYS D 100 " --> pdb=" O TYR F 35 " (cutoff:3.500A) removed outlier: 18.354A pdb=" N ALA F 37 " --> pdb=" O TYR D 98 " (cutoff:3.500A) removed outlier: 21.738A pdb=" N TYR D 98 " --> pdb=" O ALA F 37 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE D 127 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE D 106 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA D 125 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU D 122 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN D 58 " --> pdb=" O PRO D 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 134 through 141 removed outlier: 3.512A pdb=" N THR F 651 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS F 653 " --> pdb=" O PRO F 555 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLU F 655 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N GLY F 553 " --> pdb=" O GLU F 655 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 134 through 141 removed outlier: 3.512A pdb=" N THR F 651 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS F 653 " --> pdb=" O PRO F 555 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLU F 655 " --> pdb=" O GLY F 553 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N GLY F 553 " --> pdb=" O GLU F 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 537 through 543 removed outlier: 3.900A pdb=" N SER F 569 " --> pdb=" O TYR F 641 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA F 580 " --> pdb=" O VAL F 572 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLN F 574 " --> pdb=" O THR F 578 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.991A pdb=" N ILE A 127 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE A 106 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ALA A 125 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 122 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN A 58 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 11 through 13 removed outlier: 21.766A pdb=" N TYR A 98 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 18.437A pdb=" N ALA C 37 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 16.455A pdb=" N LYS A 100 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 13.214A pdb=" N TYR C 35 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ASN A 102 " --> pdb=" O ASN C 33 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASN C 33 " --> pdb=" O ASN A 102 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 104 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS C 46 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LYS C 44 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR C 38 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N PHE C 42 " --> pdb=" O TYR C 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 41 through 49 removed outlier: 4.837A pdb=" N PHE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 38 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS A 44 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 36 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 46 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 104 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASN A 33 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N ASN B 102 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 13.156A pdb=" N TYR A 35 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 16.371A pdb=" N LYS B 100 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 18.367A pdb=" N ALA A 37 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 21.789A pdb=" N TYR B 98 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 41 through 49 removed outlier: 4.837A pdb=" N PHE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 38 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LYS A 44 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 36 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 46 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLN B 104 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ASN A 33 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 10.474A pdb=" N ASN B 102 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 13.156A pdb=" N TYR A 35 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 16.371A pdb=" N LYS B 100 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 18.367A pdb=" N ALA A 37 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 21.789A pdb=" N TYR B 98 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 127 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 106 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 125 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU B 122 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN B 58 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 134 through 141 removed outlier: 3.889A pdb=" N LYS A 653 " --> pdb=" O PRO A 555 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLU A 655 " --> pdb=" O GLY A 553 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLY A 553 " --> pdb=" O GLU A 655 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 604 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 134 through 141 removed outlier: 3.889A pdb=" N LYS A 653 " --> pdb=" O PRO A 555 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N GLU A 655 " --> pdb=" O GLY A 553 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLY A 553 " --> pdb=" O GLU A 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 537 through 543 removed outlier: 3.912A pdb=" N SER A 569 " --> pdb=" O TYR A 641 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 580 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN A 574 " --> pdb=" O THR A 578 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 134 through 141 removed outlier: 3.544A pdb=" N THR B 651 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 653 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU B 655 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY B 553 " --> pdb=" O GLU B 655 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 593 " --> pdb=" O TYR B 608 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 604 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 134 through 141 removed outlier: 3.544A pdb=" N THR B 651 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS B 653 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU B 655 " --> pdb=" O GLY B 553 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N GLY B 553 " --> pdb=" O GLU B 655 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 537 through 543 removed outlier: 3.869A pdb=" N SER B 569 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA B 580 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 574 " --> pdb=" O THR B 578 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 13 removed outlier: 7.016A pdb=" N ILE C 127 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 106 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA C 125 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 122 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN C 58 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 11 through 13 removed outlier: 21.697A pdb=" N TYR C 98 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 18.287A pdb=" N ALA E 37 " --> pdb=" O TYR C 98 " (cutoff:3.500A) removed outlier: 16.317A pdb=" N LYS C 100 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 13.017A pdb=" N TYR E 35 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ASN C 102 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN E 33 " --> pdb=" O ASN C 102 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLN C 104 " --> pdb=" O LEU E 31 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS E 46 " --> pdb=" O THR E 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER E 36 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LYS E 44 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR E 38 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N PHE E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 134 through 141 removed outlier: 3.892A pdb=" N LYS C 653 " --> pdb=" O PRO C 555 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLU C 655 " --> pdb=" O GLY C 553 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N GLY C 553 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 134 through 141 removed outlier: 3.892A pdb=" N LYS C 653 " --> pdb=" O PRO C 555 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N GLU C 655 " --> pdb=" O GLY C 553 " (cutoff:3.500A) removed outlier: 9.464A pdb=" N GLY C 553 " --> pdb=" O GLU C 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 537 through 543 removed outlier: 3.916A pdb=" N SER C 569 " --> pdb=" O TYR C 641 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA C 580 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN C 574 " --> pdb=" O THR C 578 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR C 578 " --> pdb=" O GLN C 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 41 through 49 removed outlier: 4.868A pdb=" N PHE D 42 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D 38 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LYS D 44 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER D 36 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 46 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN E 104 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN D 33 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ASN E 102 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N TYR D 35 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 16.412A pdb=" N LYS E 100 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 18.337A pdb=" N ALA D 37 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 21.762A pdb=" N TYR E 98 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 41 through 49 removed outlier: 4.868A pdb=" N PHE D 42 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D 38 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LYS D 44 " --> pdb=" O SER D 36 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER D 36 " --> pdb=" O LYS D 44 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 46 " --> pdb=" O THR D 34 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN E 104 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ASN D 33 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ASN E 102 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 13.237A pdb=" N TYR D 35 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 16.412A pdb=" N LYS E 100 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 18.337A pdb=" N ALA D 37 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 21.762A pdb=" N TYR E 98 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE E 127 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA E 125 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU E 122 " --> pdb=" O PHE E 63 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN E 58 " --> pdb=" O PRO E 24 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 134 through 141 removed outlier: 3.943A pdb=" N LYS D 653 " --> pdb=" O PRO D 555 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU D 655 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLY D 553 " --> pdb=" O GLU D 655 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 134 through 141 removed outlier: 3.943A pdb=" N LYS D 653 " --> pdb=" O PRO D 555 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLU D 655 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N GLY D 553 " --> pdb=" O GLU D 655 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 537 through 543 removed outlier: 3.940A pdb=" N SER D 569 " --> pdb=" O TYR D 641 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 580 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN D 574 " --> pdb=" O THR D 578 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N THR D 578 " --> pdb=" O GLN D 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 134 through 141 removed outlier: 3.859A pdb=" N LYS E 653 " --> pdb=" O PRO E 555 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLU E 655 " --> pdb=" O GLY E 553 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLY E 553 " --> pdb=" O GLU E 655 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 604 " --> pdb=" O SER E 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 134 through 141 removed outlier: 3.859A pdb=" N LYS E 653 " --> pdb=" O PRO E 555 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLU E 655 " --> pdb=" O GLY E 553 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLY E 553 " --> pdb=" O GLU E 655 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 537 through 543 removed outlier: 3.948A pdb=" N SER E 569 " --> pdb=" O TYR E 641 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA E 580 " --> pdb=" O VAL E 572 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN E 574 " --> pdb=" O THR E 578 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1755 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: 2.16 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4582 1.34 - 1.46: 3670 1.46 - 1.58: 6579 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 14849 Sorted by residual: bond pdb=" N MET D 1 " pdb=" CA MET D 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" N MET C 1 " pdb=" CA MET C 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 14844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 19878 1.21 - 2.42: 318 2.42 - 3.62: 59 3.62 - 4.83: 23 4.83 - 6.04: 5 Bond angle restraints: 20283 Sorted by residual: angle pdb=" C GLY E 531 " pdb=" N ARG E 532 " pdb=" CA ARG E 532 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C GLY B 531 " pdb=" N ARG B 532 " pdb=" CA ARG B 532 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.44e+00 angle pdb=" N ASN D 159 " pdb=" CA ASN D 159 " pdb=" C ASN D 159 " ideal model delta sigma weight residual 114.56 110.87 3.69 1.27e+00 6.20e-01 8.44e+00 angle pdb=" N ILE B 116 " pdb=" CA ILE B 116 " pdb=" C ILE B 116 " ideal model delta sigma weight residual 111.62 109.55 2.07 7.90e-01 1.60e+00 6.84e+00 angle pdb=" N ILE D 116 " pdb=" CA ILE D 116 " pdb=" C ILE D 116 " ideal model delta sigma weight residual 111.62 109.59 2.03 7.90e-01 1.60e+00 6.63e+00 ... (remaining 20278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.86: 7986 14.86 - 29.73: 535 29.73 - 44.59: 160 44.59 - 59.45: 20 59.45 - 74.32: 15 Dihedral angle restraints: 8716 sinusoidal: 3316 harmonic: 5400 Sorted by residual: dihedral pdb=" CG LYS A 3 " pdb=" CD LYS A 3 " pdb=" CE LYS A 3 " pdb=" NZ LYS A 3 " ideal model delta sinusoidal sigma weight residual 60.00 113.62 -53.62 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CG LYS D 3 " pdb=" CD LYS D 3 " pdb=" CE LYS D 3 " pdb=" NZ LYS D 3 " ideal model delta sinusoidal sigma weight residual 60.00 113.58 -53.58 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" CA GLN B 58 " pdb=" CB GLN B 58 " pdb=" CG GLN B 58 " pdb=" CD GLN B 58 " ideal model delta sinusoidal sigma weight residual -60.00 -111.23 51.23 3 1.50e+01 4.44e-03 8.99e+00 ... (remaining 8713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1278 0.028 - 0.056: 702 0.056 - 0.083: 125 0.083 - 0.111: 110 0.111 - 0.139: 77 Chirality restraints: 2292 Sorted by residual: chirality pdb=" CA ARG B 532 " pdb=" N ARG B 532 " pdb=" C ARG B 532 " pdb=" CB ARG B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE D 607 " pdb=" N ILE D 607 " pdb=" C ILE D 607 " pdb=" CB ILE D 607 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE A 607 " pdb=" N ILE A 607 " pdb=" C ILE A 607 " pdb=" CB ILE A 607 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 2289 not shown) Planarity restraints: 2597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 606 " 0.095 9.50e-02 1.11e+02 4.30e-02 1.55e+00 pdb=" NE ARG D 606 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG D 606 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 606 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 606 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 531 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.03e+00 pdb=" C GLY E 531 " 0.018 2.00e-02 2.50e+03 pdb=" O GLY E 531 " -0.007 2.00e-02 2.50e+03 pdb=" N ARG E 532 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 531 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.01e+00 pdb=" C GLY B 531 " 0.017 2.00e-02 2.50e+03 pdb=" O GLY B 531 " -0.007 2.00e-02 2.50e+03 pdb=" N ARG B 532 " -0.006 2.00e-02 2.50e+03 ... (remaining 2594 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 75 2.60 - 3.17: 11666 3.17 - 3.75: 20774 3.75 - 4.32: 30995 4.32 - 4.90: 52756 Nonbonded interactions: 116266 Sorted by model distance: nonbonded pdb=" OG SER F 544 " pdb=" OE2 GLU F 654 " model vdw 2.019 3.040 nonbonded pdb=" OG SER C 544 " pdb=" OE2 GLU C 654 " model vdw 2.035 3.040 nonbonded pdb=" O LEU A 81 " pdb=" OH TYR A 86 " model vdw 2.041 3.040 nonbonded pdb=" OG SER E 544 " pdb=" OE2 GLU E 654 " model vdw 2.071 3.040 nonbonded pdb=" O LEU B 81 " pdb=" OH TYR B 86 " model vdw 2.072 3.040 ... (remaining 116261 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' selection = (chain 'B' and (resid 1 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 659)) selection = (chain 'C' and (resid 1 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 659)) selection = (chain 'D' and (resid 1 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 659)) selection = (chain 'E' and (resid 1 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 659)) selection = (chain 'F' and (resid 1 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 659)) } 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: 4.460 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.850 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14849 Z= 0.092 Angle : 0.451 6.040 20283 Z= 0.243 Chirality : 0.043 0.139 2292 Planarity : 0.003 0.043 2597 Dihedral : 11.618 74.318 5284 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1794 helix: -0.99 (0.38), residues: 156 sheet: 0.98 (0.20), residues: 636 loop : -0.57 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 606 TYR 0.011 0.001 TYR D 614 PHE 0.006 0.001 PHE C 126 TRP 0.007 0.001 TRP E 570 HIS 0.001 0.000 HIS C 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (14849) covalent geometry : angle 0.45142 / 0.24 (20283) hydrogen bonds : bond 0.20048 / 13.20 ( 538) hydrogen bonds : angle 8.62358 / 5.86 ( 1755) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.566 Fit side-chains REVERT: D 653 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8618 (mttt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.5317 time to fit residues: 135.6538 Evaluate side-chains 157 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.0470 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 567 ASN F 593 GLN C 567 ASN E 535 ASN E 567 ASN E 593 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.093771 restraints weight = 17831.911| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.81 r_work: 0.2908 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14849 Z= 0.116 Angle : 0.526 11.331 20283 Z= 0.275 Chirality : 0.043 0.130 2292 Planarity : 0.003 0.025 2597 Dihedral : 4.007 13.193 2016 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.75 % Allowed : 9.09 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1794 helix: -0.51 (0.41), residues: 156 sheet: 0.91 (0.19), residues: 702 loop : -0.51 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 8 TYR 0.014 0.001 TYR D 604 PHE 0.009 0.001 PHE A 126 TRP 0.008 0.001 TRP B 570 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (14849) covalent geometry : angle 0.52634 / 0.27 (20283) hydrogen bonds : bond 0.04033 / 2.70 ( 538) hydrogen bonds : angle 5.42194 / 3.66 ( 1755) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.488 Fit side-chains REVERT: F 58 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: A 32 LYS cc_start: 0.8712 (pttt) cc_final: 0.8504 (pttt) REVERT: A 58 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: A 140 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7590 (mt-10) REVERT: C 58 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8105 (tm-30) REVERT: D 58 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7884 (tt0) outliers start: 12 outliers final: 1 residues processed: 162 average time/residue: 0.4304 time to fit residues: 78.8090 Evaluate side-chains 156 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 143 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 8 optimal weight: 0.0070 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.089513 restraints weight = 17964.188| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.63 r_work: 0.2854 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14849 Z= 0.154 Angle : 0.535 10.128 20283 Z= 0.278 Chirality : 0.043 0.132 2292 Planarity : 0.003 0.025 2597 Dihedral : 4.189 13.303 2016 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.43 % Allowed : 9.40 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1794 helix: -0.33 (0.43), residues: 156 sheet: 0.99 (0.19), residues: 666 loop : -0.66 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 8 TYR 0.014 0.001 TYR D 604 PHE 0.010 0.002 PHE C 126 TRP 0.008 0.002 TRP B 570 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (14849) covalent geometry : angle 0.53510 / 0.28 (20283) hydrogen bonds : bond 0.03907 / 2.61 ( 538) hydrogen bonds : angle 5.04726 / 3.41 ( 1755) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.565 Fit side-chains REVERT: F 58 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: F 59 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8664 (pp) REVERT: A 58 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: C 58 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: C 59 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8680 (pp) REVERT: C 141 GLU cc_start: 0.7908 (pm20) cc_final: 0.7563 (pm20) REVERT: D 10 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: D 58 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8169 (tt0) outliers start: 23 outliers final: 3 residues processed: 162 average time/residue: 0.4270 time to fit residues: 77.8459 Evaluate side-chains 159 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 159 optimal weight: 0.0970 chunk 175 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN C 535 ASN E 48 GLN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.087556 restraints weight = 17918.795| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.62 r_work: 0.2823 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14849 Z= 0.180 Angle : 0.557 10.410 20283 Z= 0.287 Chirality : 0.044 0.132 2292 Planarity : 0.003 0.024 2597 Dihedral : 4.374 13.519 2016 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.62 % Allowed : 9.89 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1794 helix: -0.28 (0.43), residues: 156 sheet: 0.97 (0.19), residues: 660 loop : -0.70 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 606 TYR 0.017 0.002 TYR A 604 PHE 0.010 0.002 PHE D 126 TRP 0.008 0.002 TRP D 570 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 (14849) covalent geometry : angle 0.55682 / 0.29 (20283) hydrogen bonds : bond 0.03767 / 2.51 ( 538) hydrogen bonds : angle 4.93721 / 3.33 ( 1755) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.587 Fit side-chains REVERT: F 58 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8251 (tt0) REVERT: F 59 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 58 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: A 59 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8708 (pp) REVERT: B 1 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8373 (ttt) REVERT: C 58 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: C 141 GLU cc_start: 0.7913 (pm20) cc_final: 0.7588 (pm20) REVERT: C 625 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6871 (ptpp) REVERT: D 58 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: D 59 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8685 (pp) outliers start: 26 outliers final: 9 residues processed: 172 average time/residue: 0.4815 time to fit residues: 93.2213 Evaluate side-chains 168 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 625 LYS Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 131 optimal weight: 0.0020 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 48 GLN F 150 ASN F 535 ASN C 535 ASN D 535 ASN E 535 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.129463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.086255 restraints weight = 18069.607| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.62 r_work: 0.2798 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14849 Z= 0.221 Angle : 0.585 10.929 20283 Z= 0.302 Chirality : 0.045 0.132 2292 Planarity : 0.003 0.025 2597 Dihedral : 4.551 13.879 2016 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.24 % Allowed : 10.70 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1794 helix: 0.74 (0.51), residues: 120 sheet: 0.79 (0.18), residues: 696 loop : -0.83 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 606 TYR 0.018 0.002 TYR A 604 PHE 0.011 0.002 PHE C 126 TRP 0.008 0.002 TRP D 570 HIS 0.004 0.001 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (14849) covalent geometry : angle 0.58451 / 0.30 (20283) hydrogen bonds : bond 0.03895 / 2.58 ( 538) hydrogen bonds : angle 4.97481 / 3.35 ( 1755) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.575 Fit side-chains REVERT: F 58 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: F 59 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8696 (pp) REVERT: A 58 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 59 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 140 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: B 1 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: B 43 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8822 (mt) REVERT: C 58 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: C 59 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8717 (pp) REVERT: C 141 GLU cc_start: 0.7875 (pm20) cc_final: 0.7520 (pm20) REVERT: D 10 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8267 (pt0) REVERT: D 58 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: D 59 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8716 (pp) REVERT: E 43 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8850 (mt) outliers start: 36 outliers final: 10 residues processed: 175 average time/residue: 0.4626 time to fit residues: 91.3527 Evaluate side-chains 170 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 159 optimal weight: 0.0570 chunk 14 optimal weight: 0.0870 chunk 147 optimal weight: 7.9990 chunk 141 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN B 567 ASN C 535 ASN D 535 ASN E 535 ASN E 567 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.088752 restraints weight = 17827.257| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.69 r_work: 0.2838 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14849 Z= 0.104 Angle : 0.489 9.690 20283 Z= 0.256 Chirality : 0.042 0.125 2292 Planarity : 0.003 0.025 2597 Dihedral : 4.142 12.979 2016 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.74 % Allowed : 11.14 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1794 helix: 1.00 (0.52), residues: 120 sheet: 0.79 (0.19), residues: 636 loop : -0.76 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 606 TYR 0.011 0.001 TYR D 604 PHE 0.007 0.001 PHE D 126 TRP 0.008 0.001 TRP A 570 HIS 0.001 0.000 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (14849) covalent geometry : angle 0.48910 / 0.26 (20283) hydrogen bonds : bond 0.03276 / 2.18 ( 538) hydrogen bonds : angle 4.58738 / 3.09 ( 1755) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.529 Fit side-chains REVERT: F 43 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8828 (mt) REVERT: F 58 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: F 140 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: A 58 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: A 59 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8612 (pp) REVERT: B 1 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8345 (ttt) REVERT: C 58 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: C 59 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8616 (pp) REVERT: D 10 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: D 59 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8615 (pp) REVERT: E 43 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8817 (mt) outliers start: 28 outliers final: 10 residues processed: 173 average time/residue: 0.4647 time to fit residues: 90.2883 Evaluate side-chains 169 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 0.0970 chunk 14 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 166 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN B 567 ASN C 535 ASN D 535 ASN E 535 ASN E 567 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.091767 restraints weight = 17927.435| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.62 r_work: 0.2884 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14849 Z= 0.080 Angle : 0.452 9.101 20283 Z= 0.238 Chirality : 0.041 0.122 2292 Planarity : 0.003 0.025 2597 Dihedral : 3.822 12.330 2016 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.31 % Allowed : 11.76 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1794 helix: 1.21 (0.52), residues: 120 sheet: 0.85 (0.19), residues: 636 loop : -0.64 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 606 TYR 0.010 0.001 TYR B 131 PHE 0.007 0.001 PHE D 126 TRP 0.008 0.001 TRP C 570 HIS 0.001 0.000 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00172 / 0.08 (14849) covalent geometry : angle 0.45169 / 0.24 (20283) hydrogen bonds : bond 0.02940 / 1.95 ( 538) hydrogen bonds : angle 4.29289 / 2.91 ( 1755) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.549 Fit side-chains REVERT: F 59 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 59 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8551 (pp) REVERT: C 650 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8488 (tt) REVERT: D 10 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: D 59 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8581 (pp) outliers start: 21 outliers final: 9 residues processed: 172 average time/residue: 0.4334 time to fit residues: 84.7705 Evaluate side-chains 165 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 659 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN C 535 ASN D 535 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.085792 restraints weight = 17902.418| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.69 r_work: 0.2795 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14849 Z= 0.244 Angle : 0.588 11.849 20283 Z= 0.301 Chirality : 0.045 0.134 2292 Planarity : 0.003 0.025 2597 Dihedral : 4.459 13.823 2016 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.18 % Allowed : 10.89 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.19), residues: 1794 helix: 0.88 (0.51), residues: 120 sheet: 0.78 (0.18), residues: 708 loop : -0.66 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 606 TYR 0.021 0.002 TYR A 604 PHE 0.011 0.002 PHE B 130 TRP 0.010 0.002 TRP A 134 HIS 0.003 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.24 (14849) covalent geometry : angle 0.58805 / 0.30 (20283) hydrogen bonds : bond 0.03822 / 2.53 ( 538) hydrogen bonds : angle 4.77889 / 3.22 ( 1755) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.577 Fit side-chains REVERT: F 43 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (mt) REVERT: F 58 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8279 (tt0) REVERT: F 59 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8700 (pp) REVERT: A 58 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: A 59 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8730 (pp) REVERT: A 140 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7302 (mm-30) REVERT: B 43 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8820 (mt) REVERT: C 58 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: C 59 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8713 (pp) REVERT: D 10 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8287 (pt0) REVERT: D 58 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: D 59 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8755 (pp) outliers start: 35 outliers final: 15 residues processed: 177 average time/residue: 0.4506 time to fit residues: 90.3893 Evaluate side-chains 172 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 659 VAL Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 659 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN C 150 ASN C 535 ASN D 535 ASN E 535 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.086523 restraints weight = 17968.994| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.69 r_work: 0.2806 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14849 Z= 0.183 Angle : 0.547 10.716 20283 Z= 0.282 Chirality : 0.044 0.132 2292 Planarity : 0.003 0.027 2597 Dihedral : 4.387 13.527 2016 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.99 % Allowed : 11.20 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.19), residues: 1794 helix: -0.27 (0.44), residues: 156 sheet: 0.80 (0.18), residues: 696 loop : -0.60 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 606 TYR 0.015 0.001 TYR A 604 PHE 0.009 0.002 PHE B 126 TRP 0.008 0.002 TRP D 570 HIS 0.002 0.001 HIS C 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (14849) covalent geometry : angle 0.54699 / 0.28 (20283) hydrogen bonds : bond 0.03580 / 2.38 ( 538) hydrogen bonds : angle 4.67949 / 3.15 ( 1755) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.547 Fit side-chains REVERT: F 43 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8819 (mt) REVERT: F 58 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: F 59 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 59 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8683 (pp) REVERT: A 140 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: B 43 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8799 (mt) REVERT: C 58 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 59 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8674 (pp) REVERT: D 10 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8292 (pt0) REVERT: D 58 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8301 (tt0) REVERT: D 59 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8699 (pp) REVERT: D 140 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: E 43 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8822 (mt) outliers start: 32 outliers final: 16 residues processed: 173 average time/residue: 0.4538 time to fit residues: 88.7580 Evaluate side-chains 174 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 659 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 659 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 46 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 151 optimal weight: 0.0570 chunk 164 optimal weight: 50.0000 chunk 160 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 0.0170 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN B 567 ASN C 150 ASN C 535 ASN D 535 ASN E 535 ASN E 567 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.090624 restraints weight = 17803.559| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.70 r_work: 0.2871 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 14849 Z= 0.076 Angle : 0.460 9.488 20283 Z= 0.242 Chirality : 0.041 0.132 2292 Planarity : 0.003 0.027 2597 Dihedral : 3.940 12.423 2016 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.18 % Allowed : 12.13 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.19), residues: 1794 helix: 1.23 (0.52), residues: 120 sheet: 0.84 (0.19), residues: 636 loop : -0.64 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 606 TYR 0.010 0.001 TYR E 608 PHE 0.006 0.001 PHE B 126 TRP 0.008 0.001 TRP A 97 HIS 0.001 0.000 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00155 / 0.08 (14849) covalent geometry : angle 0.45961 / 0.24 (20283) hydrogen bonds : bond 0.02952 / 1.96 ( 538) hydrogen bonds : angle 4.29915 / 2.91 ( 1755) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3588 Ramachandran restraints generated. 1794 Oldfield, 0 Emsley, 1794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.726 Fit side-chains REVERT: F 59 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 59 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8569 (pp) REVERT: C 19 LEU cc_start: 0.9013 (pt) cc_final: 0.8771 (pp) REVERT: D 10 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: D 59 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8580 (pp) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.4383 time to fit residues: 84.5791 Evaluate side-chains 164 residues out of total 1608 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 572 VAL Chi-restraints excluded: chain F residue 659 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain E residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 136 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 101 optimal weight: 0.0670 chunk 86 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 535 ASN C 535 ASN D 535 ASN E 535 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.133794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089747 restraints weight = 17771.293| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.68 r_work: 0.2858 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14849 Z= 0.097 Angle : 0.474 9.782 20283 Z= 0.247 Chirality : 0.041 0.130 2292 Planarity : 0.003 0.027 2597 Dihedral : 3.943 12.757 2016 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.12 % Allowed : 12.32 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1794 helix: 1.25 (0.52), residues: 120 sheet: 0.88 (0.19), residues: 636 loop : -0.61 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 606 TYR 0.010 0.001 TYR A 604 PHE 0.007 0.001 PHE E 126 TRP 0.008 0.001 TRP C 570 HIS 0.001 0.000 HIS F 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (14849) covalent geometry : angle 0.47414 / 0.25 (20283) hydrogen bonds : bond 0.03058 / 2.03 ( 538) hydrogen bonds : angle 4.29307 / 2.90 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5018.45 seconds wall clock time: 86 minutes 30.72 seconds (5190.72 seconds total)