Starting phenix.real_space_refine on Tue Aug 26 14:56:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvb_36673/08_2025/8jvb_36673.map" } resolution = 2.39 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= 0.000 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 24150 2.51 5 N 6720 2.21 5 O 7308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38276 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "C" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "D" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "E" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "F" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "G" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "H" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "I" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "J" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "K" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "L" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "M" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Chain: "N" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2734 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 23, 'TRANS': 340} Chain breaks: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.22 Number of scatterers: 38276 At special positions: 0 Unit cell: (155.644, 151.636, 153.64, 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 98 16.00 O 7308 8.00 N 6720 7.00 C 24150 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 953.7 nanoseconds 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9268 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 31 sheets defined 18.7% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.727A pdb=" N ALA A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR A 146 " --> pdb=" O GLN A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 396 through 400 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 132 through 142 Processing helix chain 'B' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR B 146 " --> pdb=" O GLN B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 143 through 146' Processing helix chain 'B' and resid 396 through 400 Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 432 through 452 removed outlier: 3.737A pdb=" N GLN B 438 " --> pdb=" O GLU B 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR B 452 " --> pdb=" O GLU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR C 146 " --> pdb=" O GLN C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 396 through 400 Processing helix chain 'C' and resid 402 through 406 Processing helix chain 'C' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN C 438 " --> pdb=" O GLU C 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C 452 " --> pdb=" O GLU C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 465 removed outlier: 3.647A pdb=" N ASP C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR D 146 " --> pdb=" O GLN D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 143 through 146' Processing helix chain 'D' and resid 396 through 400 Processing helix chain 'D' and resid 402 through 406 Processing helix chain 'D' and resid 432 through 452 removed outlier: 3.737A pdb=" N GLN D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 452 " --> pdb=" O GLU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 132 through 142 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR E 146 " --> pdb=" O GLN E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 396 through 400 Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 452 " --> pdb=" O GLU E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 132 through 142 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR F 146 " --> pdb=" O GLN F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 396 through 400 Processing helix chain 'F' and resid 402 through 406 Processing helix chain 'F' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 452 " --> pdb=" O GLU F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 132 through 142 Processing helix chain 'G' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR G 146 " --> pdb=" O GLN G 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 143 through 146' Processing helix chain 'G' and resid 396 through 400 Processing helix chain 'G' and resid 402 through 406 Processing helix chain 'G' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN G 438 " --> pdb=" O GLU G 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR G 452 " --> pdb=" O GLU G 448 " (cutoff:3.500A) Processing helix chain 'G' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 132 through 142 Processing helix chain 'H' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR H 146 " --> pdb=" O GLN H 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 143 through 146' Processing helix chain 'H' and resid 396 through 400 Processing helix chain 'H' and resid 402 through 406 Processing helix chain 'H' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN H 438 " --> pdb=" O GLU H 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR H 452 " --> pdb=" O GLU H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 109 Processing helix chain 'I' and resid 132 through 142 Processing helix chain 'I' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR I 146 " --> pdb=" O GLN I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 146' Processing helix chain 'I' and resid 396 through 400 Processing helix chain 'I' and resid 402 through 406 Processing helix chain 'I' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR I 452 " --> pdb=" O GLU I 448 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP I 461 " --> pdb=" O SER I 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 109 Processing helix chain 'J' and resid 132 through 142 Processing helix chain 'J' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR J 146 " --> pdb=" O GLN J 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 143 through 146' Processing helix chain 'J' and resid 396 through 400 Processing helix chain 'J' and resid 402 through 406 Processing helix chain 'J' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN J 438 " --> pdb=" O GLU J 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 452 " --> pdb=" O GLU J 448 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 465 removed outlier: 3.647A pdb=" N ASP J 461 " --> pdb=" O SER J 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 109 Processing helix chain 'K' and resid 132 through 142 Processing helix chain 'K' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR K 146 " --> pdb=" O GLN K 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 143 through 146' Processing helix chain 'K' and resid 396 through 400 Processing helix chain 'K' and resid 402 through 406 Processing helix chain 'K' and resid 432 through 452 removed outlier: 3.737A pdb=" N GLN K 438 " --> pdb=" O GLU K 434 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR K 452 " --> pdb=" O GLU K 448 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP K 461 " --> pdb=" O SER K 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 109 Processing helix chain 'L' and resid 132 through 142 Processing helix chain 'L' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR L 146 " --> pdb=" O GLN L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 143 through 146' Processing helix chain 'L' and resid 396 through 400 Processing helix chain 'L' and resid 402 through 406 Processing helix chain 'L' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN L 438 " --> pdb=" O GLU L 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR L 452 " --> pdb=" O GLU L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 465 removed outlier: 3.647A pdb=" N ASP L 461 " --> pdb=" O SER L 457 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 109 Processing helix chain 'M' and resid 132 through 142 Processing helix chain 'M' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR M 146 " --> pdb=" O GLN M 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 143 through 146' Processing helix chain 'M' and resid 396 through 400 Processing helix chain 'M' and resid 402 through 406 Processing helix chain 'M' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN M 438 " --> pdb=" O GLU M 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR M 452 " --> pdb=" O GLU M 448 " (cutoff:3.500A) Processing helix chain 'M' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP M 461 " --> pdb=" O SER M 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 109 Processing helix chain 'N' and resid 132 through 142 Processing helix chain 'N' and resid 143 through 146 removed outlier: 3.734A pdb=" N TYR N 146 " --> pdb=" O GLN N 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 143 through 146' Processing helix chain 'N' and resid 396 through 400 Processing helix chain 'N' and resid 402 through 406 Processing helix chain 'N' and resid 432 through 452 removed outlier: 3.736A pdb=" N GLN N 438 " --> pdb=" O GLU N 434 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR N 452 " --> pdb=" O GLU N 448 " (cutoff:3.500A) Processing helix chain 'N' and resid 457 through 465 removed outlier: 3.646A pdb=" N ASP N 461 " --> pdb=" O SER N 457 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.633A pdb=" N ASP A 127 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 119 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 124 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 185 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 163 through 185 current: chain 'A' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 408 through 428 current: chain 'B' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 408 through 428 current: chain 'C' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 408 through 428 current: chain 'D' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 408 through 428 current: chain 'E' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 408 through 428 current: chain 'F' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 408 through 428 current: chain 'G' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 408 through 428 current: chain 'H' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 408 through 428 current: chain 'I' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 408 through 428 current: chain 'J' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 408 through 428 current: chain 'K' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 408 through 428 current: chain 'L' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 408 through 428 current: chain 'M' and resid 408 through 428 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 408 through 428 current: chain 'N' and resid 408 through 428 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 201 removed outlier: 6.522A pdb=" N PHE A 253 " --> pdb=" O PHE N 200 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE N 253 " --> pdb=" O PHE M 200 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE M 253 " --> pdb=" O PHE L 200 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE L 253 " --> pdb=" O PHE K 200 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE K 253 " --> pdb=" O PHE J 200 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE J 253 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE I 253 " --> pdb=" O PHE H 200 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE H 253 " --> pdb=" O PHE G 200 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE G 253 " --> pdb=" O PHE F 200 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE F 253 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE E 253 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE D 253 " --> pdb=" O PHE C 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE C 253 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 253 " --> pdb=" O PHE A 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208 Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 299 removed outlier: 19.529A pdb=" N VAL A 312 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 22.528A pdb=" N THR A 348 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR A 314 " --> pdb=" O PRO A 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP A 316 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE A 344 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 359 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ALA A 347 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL A 357 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 19.527A pdb=" N VAL B 312 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 22.528A pdb=" N THR B 348 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR B 314 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP B 316 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE B 344 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 359 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ALA B 347 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL B 357 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL C 312 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR C 348 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR C 314 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP C 316 " --> pdb=" O ILE C 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE C 344 " --> pdb=" O ASP C 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 359 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ALA C 347 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL C 357 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 19.528A pdb=" N VAL D 312 " --> pdb=" O THR D 348 " (cutoff:3.500A) removed outlier: 22.530A pdb=" N THR D 348 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR D 314 " --> pdb=" O PRO D 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP D 316 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE D 344 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 359 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA D 347 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL D 357 " --> pdb=" O ALA D 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL E 312 " --> pdb=" O THR E 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR E 348 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR E 314 " --> pdb=" O PRO E 346 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ASP E 316 " --> pdb=" O ILE E 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE E 344 " --> pdb=" O ASP E 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E 359 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA E 347 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL E 357 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 19.528A pdb=" N VAL F 312 " --> pdb=" O THR F 348 " (cutoff:3.500A) removed outlier: 22.528A pdb=" N THR F 348 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR F 314 " --> pdb=" O PRO F 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP F 316 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE F 344 " --> pdb=" O ASP F 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY F 359 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA F 347 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 10.715A pdb=" N VAL F 357 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 19.528A pdb=" N VAL G 312 " --> pdb=" O THR G 348 " (cutoff:3.500A) removed outlier: 22.528A pdb=" N THR G 348 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR G 314 " --> pdb=" O PRO G 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP G 316 " --> pdb=" O ILE G 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE G 344 " --> pdb=" O ASP G 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY G 359 " --> pdb=" O ASP G 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA G 347 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL G 357 " --> pdb=" O ALA G 347 " (cutoff:3.500A) removed outlier: 19.528A pdb=" N VAL H 312 " --> pdb=" O THR H 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR H 348 " --> pdb=" O VAL H 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR H 314 " --> pdb=" O PRO H 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP H 316 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE H 344 " --> pdb=" O ASP H 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY H 359 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA H 347 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL H 357 " --> pdb=" O ALA H 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL I 312 " --> pdb=" O THR I 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR I 348 " --> pdb=" O VAL I 312 " (cutoff:3.500A) removed outlier: 19.956A pdb=" N TYR I 314 " --> pdb=" O PRO I 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP I 316 " --> pdb=" O ILE I 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE I 344 " --> pdb=" O ASP I 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY I 359 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA I 347 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL I 357 " --> pdb=" O ALA I 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL J 312 " --> pdb=" O THR J 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR J 348 " --> pdb=" O VAL J 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR J 314 " --> pdb=" O PRO J 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP J 316 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE J 344 " --> pdb=" O ASP J 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY J 359 " --> pdb=" O ASP J 345 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ALA J 347 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL J 357 " --> pdb=" O ALA J 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL K 312 " --> pdb=" O THR K 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR K 348 " --> pdb=" O VAL K 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR K 314 " --> pdb=" O PRO K 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP K 316 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE K 344 " --> pdb=" O ASP K 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY K 359 " --> pdb=" O ASP K 345 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ALA K 347 " --> pdb=" O VAL K 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL K 357 " --> pdb=" O ALA K 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL L 312 " --> pdb=" O THR L 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR L 348 " --> pdb=" O VAL L 312 " (cutoff:3.500A) removed outlier: 19.957A pdb=" N TYR L 314 " --> pdb=" O PRO L 346 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP L 316 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N ILE L 344 " --> pdb=" O ASP L 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY L 359 " --> pdb=" O ASP L 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA L 347 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL L 357 " --> pdb=" O ALA L 347 " (cutoff:3.500A) removed outlier: 19.529A pdb=" N VAL M 312 " --> pdb=" O THR M 348 " (cutoff:3.500A) removed outlier: 22.529A pdb=" N THR M 348 " --> pdb=" O VAL M 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR M 314 " --> pdb=" O PRO M 346 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ASP M 316 " --> pdb=" O ILE M 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE M 344 " --> pdb=" O ASP M 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY M 359 " --> pdb=" O ASP M 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA M 347 " --> pdb=" O VAL M 357 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N VAL M 357 " --> pdb=" O ALA M 347 " (cutoff:3.500A) removed outlier: 19.528A pdb=" N VAL N 312 " --> pdb=" O THR N 348 " (cutoff:3.500A) removed outlier: 22.528A pdb=" N THR N 348 " --> pdb=" O VAL N 312 " (cutoff:3.500A) removed outlier: 19.955A pdb=" N TYR N 314 " --> pdb=" O PRO N 346 " (cutoff:3.500A) removed outlier: 13.411A pdb=" N ASP N 316 " --> pdb=" O ILE N 344 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ILE N 344 " --> pdb=" O ASP N 316 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY N 359 " --> pdb=" O ASP N 345 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N ALA N 347 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 10.716A pdb=" N VAL N 357 " --> pdb=" O ALA N 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.633A pdb=" N ASP B 127 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 119 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 125 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 124 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AA8, first strand: chain 'C' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP C 127 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 119 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C 125 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL C 124 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP D 127 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 119 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 125 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 124 " --> pdb=" O ILE D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 205 through 208 Processing sheet with id=AB3, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP E 127 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL E 119 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL E 125 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL E 124 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 205 through 208 Processing sheet with id=AB5, first strand: chain 'F' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP F 127 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL F 119 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 125 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL F 124 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 205 through 208 Processing sheet with id=AB7, first strand: chain 'G' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP G 127 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL G 119 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 125 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL G 124 " --> pdb=" O ILE G 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 205 through 208 Processing sheet with id=AB9, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP H 127 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL H 119 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL H 125 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL H 124 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 205 through 208 Processing sheet with id=AC2, first strand: chain 'I' and resid 117 through 119 removed outlier: 3.631A pdb=" N ASP I 127 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I 119 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL I 125 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL I 124 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 205 through 208 Processing sheet with id=AC4, first strand: chain 'J' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP J 127 " --> pdb=" O ILE J 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 119 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL J 125 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL J 124 " --> pdb=" O ILE J 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 205 through 208 Processing sheet with id=AC6, first strand: chain 'K' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP K 127 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL K 119 " --> pdb=" O VAL K 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL K 125 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL K 124 " --> pdb=" O ILE K 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 205 through 208 Processing sheet with id=AC8, first strand: chain 'L' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP L 127 " --> pdb=" O ILE L 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL L 119 " --> pdb=" O VAL L 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL L 125 " --> pdb=" O VAL L 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL L 124 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 205 through 208 Processing sheet with id=AD1, first strand: chain 'M' and resid 117 through 119 removed outlier: 3.633A pdb=" N ASP M 127 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL M 119 " --> pdb=" O VAL M 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL M 125 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL M 124 " --> pdb=" O ILE M 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 205 through 208 Processing sheet with id=AD3, first strand: chain 'N' and resid 117 through 119 removed outlier: 3.632A pdb=" N ASP N 127 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL N 119 " --> pdb=" O VAL N 125 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL N 125 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL N 124 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 205 through 208 1372 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12986 1.34 - 1.45: 3544 1.45 - 1.57: 22180 1.57 - 1.69: 0 1.69 - 1.80: 196 Bond restraints: 38906 Sorted by residual: bond pdb=" CA ARG K 245 " pdb=" C ARG K 245 " ideal model delta sigma weight residual 1.521 1.473 0.048 1.08e-02 8.57e+03 1.96e+01 bond pdb=" CA ARG C 245 " pdb=" C ARG C 245 " ideal model delta sigma weight residual 1.521 1.473 0.048 1.08e-02 8.57e+03 1.96e+01 bond pdb=" CA ARG H 245 " pdb=" C ARG H 245 " ideal model delta sigma weight residual 1.521 1.473 0.048 1.08e-02 8.57e+03 1.96e+01 bond pdb=" CA ARG I 245 " pdb=" C ARG I 245 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.08e-02 8.57e+03 1.91e+01 bond pdb=" CA ARG D 245 " pdb=" C ARG D 245 " ideal model delta sigma weight residual 1.521 1.474 0.047 1.08e-02 8.57e+03 1.89e+01 ... (remaining 38901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 52243 2.25 - 4.50: 565 4.50 - 6.75: 84 6.75 - 9.00: 56 9.00 - 11.25: 14 Bond angle restraints: 52962 Sorted by residual: angle pdb=" C ARG J 245 " pdb=" N PRO J 246 " pdb=" CA PRO J 246 " ideal model delta sigma weight residual 119.84 112.21 7.63 1.25e+00 6.40e-01 3.73e+01 angle pdb=" C ARG E 245 " pdb=" N PRO E 246 " pdb=" CA PRO E 246 " ideal model delta sigma weight residual 119.84 112.22 7.62 1.25e+00 6.40e-01 3.72e+01 angle pdb=" C ARG L 245 " pdb=" N PRO L 246 " pdb=" CA PRO L 246 " ideal model delta sigma weight residual 119.84 112.22 7.62 1.25e+00 6.40e-01 3.72e+01 angle pdb=" C ARG D 245 " pdb=" N PRO D 246 " pdb=" CA PRO D 246 " ideal model delta sigma weight residual 119.84 112.23 7.61 1.25e+00 6.40e-01 3.71e+01 angle pdb=" C ARG N 245 " pdb=" N PRO N 246 " pdb=" CA PRO N 246 " ideal model delta sigma weight residual 119.84 112.23 7.61 1.25e+00 6.40e-01 3.71e+01 ... (remaining 52957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 20609 18.00 - 36.00: 2066 36.00 - 54.00: 607 54.00 - 72.00: 252 72.00 - 90.00: 70 Dihedral angle restraints: 23604 sinusoidal: 9212 harmonic: 14392 Sorted by residual: dihedral pdb=" CA PRO N 246 " pdb=" C PRO N 246 " pdb=" N ILE N 247 " pdb=" CA ILE N 247 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO K 246 " pdb=" C PRO K 246 " pdb=" N ILE K 247 " pdb=" CA ILE K 247 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA PRO I 246 " pdb=" C PRO I 246 " pdb=" N ILE I 247 " pdb=" CA ILE I 247 " ideal model delta harmonic sigma weight residual 180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 23601 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5612 0.075 - 0.151: 680 0.151 - 0.226: 8 0.226 - 0.302: 0 0.302 - 0.377: 14 Chirality restraints: 6314 Sorted by residual: chirality pdb=" CA ARG K 245 " pdb=" N ARG K 245 " pdb=" C ARG K 245 " pdb=" CB ARG K 245 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ARG D 245 " pdb=" N ARG D 245 " pdb=" C ARG D 245 " pdb=" CB ARG D 245 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ARG N 245 " pdb=" N ARG N 245 " pdb=" C ARG N 245 " pdb=" CB ARG N 245 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 6311 not shown) Planarity restraints: 6958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 105 " 0.161 9.50e-02 1.11e+02 7.30e-02 4.65e+00 pdb=" NE ARG M 105 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG M 105 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG M 105 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG M 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 105 " 0.162 9.50e-02 1.11e+02 7.32e-02 4.64e+00 pdb=" NE ARG H 105 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 105 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG H 105 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 105 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 105 " 0.162 9.50e-02 1.11e+02 7.34e-02 4.63e+00 pdb=" NE ARG C 105 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 105 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 105 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 6955 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 13260 2.87 - 3.38: 33233 3.38 - 3.89: 61630 3.89 - 4.39: 71959 4.39 - 4.90: 125461 Nonbonded interactions: 305543 Sorted by model distance: nonbonded pdb=" NE2 GLN M 300 " pdb=" O VAL N 312 " model vdw 2.367 3.120 nonbonded pdb=" NE2 GLN B 300 " pdb=" O VAL C 312 " model vdw 2.367 3.120 nonbonded pdb=" NE2 GLN G 300 " pdb=" O VAL H 312 " model vdw 2.375 3.120 nonbonded pdb=" O ASN B 370 " pdb=" ND2 ASN B 370 " model vdw 2.375 3.120 nonbonded pdb=" NE2 GLN D 300 " pdb=" O VAL E 312 " model vdw 2.375 3.120 ... (remaining 305538 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 10.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 31.750 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 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 : 0.004 0.049 38906 Z= 0.195 Angle : 0.662 11.254 52962 Z= 0.361 Chirality : 0.048 0.377 6314 Planarity : 0.006 0.073 6958 Dihedral : 17.857 89.996 14336 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.08 % Allowed : 23.67 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.12), residues: 5012 helix: 1.44 (0.18), residues: 714 sheet: 0.00 (0.10), residues: 2632 loop : -0.34 (0.16), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG M 105 TYR 0.006 0.001 TYR E 314 PHE 0.006 0.001 PHE D 200 TRP 0.007 0.001 TRP D 185 HIS 0.003 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00364 (38906) covalent geometry : angle 0.66215 (52962) hydrogen bonds : bond 0.24825 ( 1372) hydrogen bonds : angle 8.17281 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 495 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ARG cc_start: 0.8714 (ptp-110) cc_final: 0.8470 (mtp85) REVERT: A 245 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7320 (mmm-85) REVERT: B 245 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7323 (mmm-85) REVERT: C 245 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7293 (mmm-85) REVERT: D 245 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7387 (mmm-85) REVERT: E 245 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7350 (mmm-85) REVERT: F 245 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7337 (mmm-85) REVERT: G 140 ARG cc_start: 0.8729 (ptp-110) cc_final: 0.8481 (mtm180) REVERT: G 245 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7375 (mmm-85) REVERT: H 140 ARG cc_start: 0.8714 (ptp-110) cc_final: 0.8468 (mtp85) REVERT: H 245 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7309 (mmm-85) REVERT: I 245 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7370 (mmm-85) REVERT: J 245 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7277 (mmm-85) REVERT: K 245 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7319 (mmm-85) REVERT: L 245 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7350 (mmm-85) REVERT: N 140 ARG cc_start: 0.8746 (ptp-110) cc_final: 0.8428 (mtm180) REVERT: N 245 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7357 (mmm-85) outliers start: 129 outliers final: 75 residues processed: 609 average time/residue: 0.6420 time to fit residues: 470.7079 Evaluate side-chains 553 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 465 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 245 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 418 ASP Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 245 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 457 SER Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 418 ASP Chi-restraints excluded: chain G residue 457 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 370 ASN Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 457 SER Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 245 ARG Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 418 ASP Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 418 ASP Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 245 ARG Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 418 ASP Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 418 ASP Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 245 ARG Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 418 ASP Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 245 ARG Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 418 ASP Chi-restraints excluded: chain N residue 457 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN ** D 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 370 ASN E 123 HIS E 370 ASN F 123 HIS F 370 ASN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN G 370 ASN I 277 ASN I 370 ASN J 277 ASN J 370 ASN ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 370 ASN ** L 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 277 ASN L 370 ASN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 277 ASN M 370 ASN ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 370 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.069860 restraints weight = 56858.131| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.22 r_work: 0.2634 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 38906 Z= 0.178 Angle : 0.645 6.468 52962 Z= 0.340 Chirality : 0.047 0.206 6314 Planarity : 0.006 0.048 6958 Dihedral : 7.528 59.633 5550 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.32 % Allowed : 21.67 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.12), residues: 5012 helix: 2.25 (0.19), residues: 756 sheet: -0.00 (0.10), residues: 2576 loop : -0.50 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 105 TYR 0.011 0.002 TYR J 314 PHE 0.009 0.001 PHE J 200 TRP 0.008 0.001 TRP F 185 HIS 0.004 0.002 HIS L 123 Details of bonding type rmsd covalent geometry : bond 0.00423 (38906) covalent geometry : angle 0.64532 (52962) hydrogen bonds : bond 0.05239 ( 1372) hydrogen bonds : angle 5.46050 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 469 time to evaluate : 1.381 Fit side-chains REVERT: A 231 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8651 (mt) REVERT: A 245 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7303 (mmm-85) REVERT: B 140 ARG cc_start: 0.9105 (ptp-110) cc_final: 0.8787 (mtp85) REVERT: C 245 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.6968 (mmm-85) REVERT: C 321 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9135 (mp) REVERT: D 217 GLN cc_start: 0.8853 (mt0) cc_final: 0.8619 (mt0) REVERT: D 231 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8611 (mt) REVERT: D 245 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7908 (mmm-85) REVERT: E 245 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7141 (mmm-85) REVERT: G 140 ARG cc_start: 0.8916 (ptp-110) cc_final: 0.8676 (mtm180) REVERT: G 245 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7480 (mmm-85) REVERT: G 320 LYS cc_start: 0.9320 (ttmt) cc_final: 0.8986 (tttt) REVERT: H 231 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8651 (mt) REVERT: H 245 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7305 (mmm-85) REVERT: I 140 ARG cc_start: 0.9117 (ptp-110) cc_final: 0.8837 (mtp85) REVERT: J 140 ARG cc_start: 0.9000 (ptp-110) cc_final: 0.8765 (mtm180) REVERT: J 245 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.6971 (mmm-85) REVERT: J 321 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9137 (mp) REVERT: K 231 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8609 (mt) REVERT: K 245 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7945 (mmm-85) REVERT: L 245 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7149 (mmm-85) REVERT: N 245 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7343 (mmm-85) REVERT: N 320 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8986 (tttt) outliers start: 181 outliers final: 74 residues processed: 609 average time/residue: 0.6989 time to fit residues: 510.0432 Evaluate side-chains 552 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 462 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 397 LEU Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 313 THR Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 245 ARG Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 274 LEU Chi-restraints excluded: chain M residue 343 ASP Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 245 ARG Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 320 optimal weight: 6.9990 chunk 337 optimal weight: 7.9990 chunk 486 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 423 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN B 370 ASN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 ASN D 370 ASN E 370 ASN F 370 ASN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 188 GLN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 188 GLN M 370 ASN ** N 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 GLN N 277 ASN N 370 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.068871 restraints weight = 56699.546| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.20 r_work: 0.2611 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 38906 Z= 0.228 Angle : 0.659 6.935 52962 Z= 0.349 Chirality : 0.048 0.208 6314 Planarity : 0.005 0.043 6958 Dihedral : 6.891 59.598 5482 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.47 % Allowed : 20.76 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.12), residues: 5012 helix: 2.53 (0.20), residues: 756 sheet: -0.06 (0.10), residues: 2576 loop : -0.70 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 105 TYR 0.011 0.002 TYR L 314 PHE 0.009 0.001 PHE C 200 TRP 0.009 0.001 TRP M 185 HIS 0.006 0.003 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00551 (38906) covalent geometry : angle 0.65889 (52962) hydrogen bonds : bond 0.05487 ( 1372) hydrogen bonds : angle 5.32993 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 458 time to evaluate : 1.280 Fit side-chains REVERT: A 231 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8610 (mt) REVERT: A 245 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7395 (mmm-85) REVERT: A 321 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9070 (mp) REVERT: B 140 ARG cc_start: 0.9098 (ptp-110) cc_final: 0.8817 (mtp85) REVERT: B 321 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9064 (mp) REVERT: C 245 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7008 (mmm-85) REVERT: C 321 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9094 (mp) REVERT: D 217 GLN cc_start: 0.8832 (mt0) cc_final: 0.8619 (mt0) REVERT: D 231 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8647 (mt) REVERT: D 321 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9145 (mp) REVERT: E 231 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8590 (mt) REVERT: E 245 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.6815 (mmm-85) REVERT: E 321 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9083 (mp) REVERT: F 231 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8617 (mt) REVERT: F 321 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9097 (mp) REVERT: G 102 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: G 245 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7405 (mmm-85) REVERT: G 320 LYS cc_start: 0.9328 (ttmt) cc_final: 0.8985 (tttt) REVERT: G 321 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9166 (mp) REVERT: H 231 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8606 (mt) REVERT: H 245 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7518 (mmm-85) REVERT: H 321 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9067 (mp) REVERT: I 140 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8813 (mtp85) REVERT: I 321 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9068 (mp) REVERT: J 245 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7054 (mmm-85) REVERT: J 321 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9104 (mp) REVERT: K 231 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8646 (mt) REVERT: K 321 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9146 (mp) REVERT: L 231 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8622 (mt) REVERT: L 245 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.6898 (mmm-85) REVERT: L 321 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9085 (mp) REVERT: M 231 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8617 (mt) REVERT: M 321 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9097 (mp) REVERT: N 102 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: N 245 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7367 (mmm-85) REVERT: N 320 LYS cc_start: 0.9331 (ttmt) cc_final: 0.8988 (tttt) REVERT: N 321 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9167 (mp) outliers start: 229 outliers final: 99 residues processed: 638 average time/residue: 0.6396 time to fit residues: 496.4568 Evaluate side-chains 582 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 451 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 343 ASP Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 245 ARG Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 363 ARG Chi-restraints excluded: chain K residue 418 ASP Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 343 ASP Chi-restraints excluded: chain L residue 353 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 321 LEU Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 102 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 245 ARG Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 321 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 192 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 415 optimal weight: 0.9990 chunk 494 optimal weight: 0.6980 chunk 251 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 407 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 326 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 370 ASN B 277 ASN B 370 ASN C 213 GLN C 277 ASN C 370 ASN D 370 ASN E 277 ASN E 370 ASN F 277 ASN F 370 ASN G 370 ASN H 277 ASN H 370 ASN I 370 ASN J 370 ASN K 277 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.071722 restraints weight = 56629.184| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.20 r_work: 0.2668 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38906 Z= 0.107 Angle : 0.567 6.043 52962 Z= 0.298 Chirality : 0.046 0.172 6314 Planarity : 0.005 0.053 6958 Dihedral : 6.416 59.951 5474 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.59 % Allowed : 21.98 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.12), residues: 5012 helix: 2.84 (0.20), residues: 756 sheet: 0.01 (0.10), residues: 2576 loop : -0.53 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 105 TYR 0.007 0.001 TYR G 314 PHE 0.006 0.001 PHE C 200 TRP 0.007 0.001 TRP M 185 HIS 0.006 0.002 HIS H 123 Details of bonding type rmsd covalent geometry : bond 0.00250 (38906) covalent geometry : angle 0.56684 (52962) hydrogen bonds : bond 0.03904 ( 1372) hydrogen bonds : angle 4.91256 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 475 time to evaluate : 1.019 Fit side-chains REVERT: A 245 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7862 (mmm-85) REVERT: A 321 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9117 (mp) REVERT: B 140 ARG cc_start: 0.9042 (ptp-110) cc_final: 0.8807 (mtp85) REVERT: B 231 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8711 (mt) REVERT: B 321 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9107 (mp) REVERT: C 245 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7966 (mmm-85) REVERT: D 217 GLN cc_start: 0.8804 (mt0) cc_final: 0.8580 (mt0) REVERT: D 321 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9154 (mp) REVERT: E 105 ARG cc_start: 0.9087 (ttm110) cc_final: 0.8883 (ttm110) REVERT: E 231 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8554 (mt) REVERT: E 245 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7387 (mmm-85) REVERT: E 321 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9105 (mp) REVERT: F 140 ARG cc_start: 0.9029 (mtm-85) cc_final: 0.8797 (mtm180) REVERT: F 231 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8568 (mt) REVERT: G 320 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9001 (tttt) REVERT: H 245 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7860 (mmm-85) REVERT: H 321 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9120 (mp) REVERT: I 140 ARG cc_start: 0.9029 (ptp-110) cc_final: 0.8809 (mtp85) REVERT: I 231 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8709 (mt) REVERT: I 321 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9118 (mp) REVERT: J 245 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7961 (mmm-85) REVERT: K 217 GLN cc_start: 0.8794 (mt0) cc_final: 0.8568 (mt0) REVERT: K 321 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9157 (mp) REVERT: L 105 ARG cc_start: 0.9100 (ttm110) cc_final: 0.8895 (ttm110) REVERT: L 231 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8556 (mt) REVERT: L 245 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7390 (mmm-85) REVERT: L 321 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9106 (mp) REVERT: M 140 ARG cc_start: 0.9033 (mtm-85) cc_final: 0.8801 (mtm180) REVERT: M 231 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8567 (mt) REVERT: N 320 LYS cc_start: 0.9328 (ttmt) cc_final: 0.8997 (tttt) outliers start: 192 outliers final: 94 residues processed: 622 average time/residue: 0.6324 time to fit residues: 472.4285 Evaluate side-chains 578 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 464 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 ARG Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 ARG Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 343 ASP Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 353 ASN Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 363 ARG Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 313 THR Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 353 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 353 ASN Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 363 ARG Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 236 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 369 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 413 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 291 optimal weight: 8.9990 chunk 176 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN A 370 ASN B 188 GLN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 188 GLN H 370 ASN I 188 GLN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.068649 restraints weight = 56742.734| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.20 r_work: 0.2607 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 38906 Z= 0.264 Angle : 0.672 7.151 52962 Z= 0.357 Chirality : 0.049 0.207 6314 Planarity : 0.005 0.065 6958 Dihedral : 6.655 59.648 5462 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.06 % Allowed : 21.83 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.12), residues: 5012 helix: 2.66 (0.20), residues: 756 sheet: -0.09 (0.10), residues: 2576 loop : -0.68 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 105 TYR 0.011 0.002 TYR L 314 PHE 0.010 0.001 PHE N 200 TRP 0.009 0.001 TRP F 185 HIS 0.008 0.004 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00639 (38906) covalent geometry : angle 0.67217 (52962) hydrogen bonds : bond 0.05286 ( 1372) hydrogen bonds : angle 5.19844 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 459 time to evaluate : 1.030 Fit side-chains REVERT: A 102 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: A 231 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 245 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7458 (mmm-85) REVERT: A 321 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9059 (mp) REVERT: B 102 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: B 140 ARG cc_start: 0.9059 (ptp-110) cc_final: 0.8816 (mtp85) REVERT: B 321 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9051 (mp) REVERT: C 102 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8498 (tp30) REVERT: C 245 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.6748 (mmm-85) REVERT: C 321 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9095 (mp) REVERT: D 102 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: D 231 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8637 (mt) REVERT: D 321 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9149 (mp) REVERT: E 105 ARG cc_start: 0.9085 (ttm110) cc_final: 0.8840 (ttm110) REVERT: E 231 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8592 (mt) REVERT: E 245 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7283 (mmm-85) REVERT: E 321 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9078 (mp) REVERT: F 102 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: F 140 ARG cc_start: 0.9034 (mtm-85) cc_final: 0.8775 (mtm180) REVERT: F 231 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8588 (mt) REVERT: G 320 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9010 (ttpt) REVERT: H 231 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8666 (mt) REVERT: H 245 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7458 (mmm-85) REVERT: H 321 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9056 (mp) REVERT: I 102 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8616 (tp30) REVERT: I 140 ARG cc_start: 0.9062 (ptp-110) cc_final: 0.8811 (mtp85) REVERT: I 321 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9053 (mp) REVERT: J 102 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8490 (tp30) REVERT: J 245 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.6798 (mmm-85) REVERT: J 321 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9102 (mp) REVERT: K 102 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8412 (tp30) REVERT: K 217 GLN cc_start: 0.8781 (mt0) cc_final: 0.8553 (mt0) REVERT: K 231 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8640 (mt) REVERT: K 321 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9152 (mp) REVERT: L 105 ARG cc_start: 0.9076 (ttm110) cc_final: 0.8823 (ttm110) REVERT: L 231 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8592 (mt) REVERT: L 245 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7280 (mmm-85) REVERT: L 321 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9077 (mp) REVERT: M 102 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: M 231 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8592 (mt) REVERT: N 320 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9001 (ttpt) outliers start: 212 outliers final: 98 residues processed: 631 average time/residue: 0.5962 time to fit residues: 458.8751 Evaluate side-chains 585 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 454 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 418 ASP Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 363 ARG Chi-restraints excluded: chain K residue 418 ASP Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 353 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 418 ASP Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 277 optimal weight: 4.9990 chunk 288 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 266 optimal weight: 0.0020 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.070112 restraints weight = 56527.939| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.20 r_work: 0.2636 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 38906 Z= 0.155 Angle : 0.599 6.732 52962 Z= 0.317 Chirality : 0.047 0.187 6314 Planarity : 0.005 0.071 6958 Dihedral : 6.462 59.307 5462 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.66 % Allowed : 23.46 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.12), residues: 5012 helix: 2.81 (0.20), residues: 756 sheet: -0.06 (0.10), residues: 2576 loop : -0.63 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 105 TYR 0.009 0.001 TYR L 314 PHE 0.008 0.001 PHE C 200 TRP 0.008 0.001 TRP I 185 HIS 0.005 0.003 HIS H 123 Details of bonding type rmsd covalent geometry : bond 0.00375 (38906) covalent geometry : angle 0.59943 (52962) hydrogen bonds : bond 0.04417 ( 1372) hydrogen bonds : angle 5.01087 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 455 time to evaluate : 1.601 Fit side-chains REVERT: A 231 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 245 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7528 (mmm-85) REVERT: A 321 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 140 ARG cc_start: 0.9039 (ptp-110) cc_final: 0.8784 (mtp85) REVERT: B 231 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 321 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9074 (mp) REVERT: C 231 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 245 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7916 (mmm-85) REVERT: C 321 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9117 (mp) REVERT: D 217 GLN cc_start: 0.8771 (mt0) cc_final: 0.8523 (mt0) REVERT: D 321 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9141 (mp) REVERT: E 231 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8570 (mt) REVERT: E 245 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7206 (mmm-85) REVERT: E 321 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9087 (mp) REVERT: F 231 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8576 (mt) REVERT: G 320 LYS cc_start: 0.9333 (ttmt) cc_final: 0.9004 (ttpt) REVERT: H 231 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8606 (mt) REVERT: H 245 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7510 (mmm-85) REVERT: H 321 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9079 (mp) REVERT: I 140 ARG cc_start: 0.9024 (ptp-110) cc_final: 0.8774 (mtp85) REVERT: I 321 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9082 (mp) REVERT: J 231 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8567 (mt) REVERT: J 245 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7906 (mmm-85) REVERT: J 321 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9121 (mp) REVERT: K 217 GLN cc_start: 0.8745 (mt0) cc_final: 0.8516 (mt0) REVERT: K 321 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9143 (mp) REVERT: L 231 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8573 (mt) REVERT: L 245 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7199 (mmm-85) REVERT: L 321 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9090 (mp) REVERT: M 231 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8578 (mt) REVERT: N 320 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9000 (ttpt) outliers start: 153 outliers final: 85 residues processed: 568 average time/residue: 0.6704 time to fit residues: 458.6212 Evaluate side-chains 564 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 454 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 245 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 245 ARG Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 418 ASP Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 353 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 343 ASP Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 353 ASN Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 27 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 292 optimal weight: 9.9990 chunk 265 optimal weight: 0.5980 chunk 272 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.070163 restraints weight = 56783.194| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.21 r_work: 0.2636 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 38906 Z= 0.159 Angle : 0.601 6.861 52962 Z= 0.317 Chirality : 0.047 0.180 6314 Planarity : 0.005 0.074 6958 Dihedral : 6.360 58.925 5460 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.09 % Allowed : 23.08 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.12), residues: 5012 helix: 2.89 (0.20), residues: 756 sheet: -0.06 (0.10), residues: 2576 loop : -0.58 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG L 105 TYR 0.009 0.001 TYR E 314 PHE 0.008 0.001 PHE J 200 TRP 0.007 0.001 TRP F 185 HIS 0.005 0.003 HIS H 123 Details of bonding type rmsd covalent geometry : bond 0.00382 (38906) covalent geometry : angle 0.60060 (52962) hydrogen bonds : bond 0.04368 ( 1372) hydrogen bonds : angle 4.97710 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 456 time to evaluate : 1.449 Fit side-chains REVERT: A 199 ASP cc_start: 0.8384 (m-30) cc_final: 0.8090 (m-30) REVERT: A 245 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7436 (mmm-85) REVERT: A 321 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9082 (mp) REVERT: B 140 ARG cc_start: 0.9023 (ptp-110) cc_final: 0.8794 (mtp85) REVERT: B 231 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8733 (mt) REVERT: B 321 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9065 (mp) REVERT: C 231 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8581 (mt) REVERT: C 321 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9115 (mp) REVERT: D 217 GLN cc_start: 0.8761 (mt0) cc_final: 0.8519 (mt0) REVERT: D 231 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8593 (mt) REVERT: D 321 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9138 (mp) REVERT: E 231 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8582 (mt) REVERT: E 245 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6687 (mmm-85) REVERT: E 321 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9083 (mp) REVERT: F 231 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8568 (mt) REVERT: G 320 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9005 (ttpt) REVERT: H 199 ASP cc_start: 0.8385 (m-30) cc_final: 0.8090 (m-30) REVERT: H 245 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7433 (mmm-85) REVERT: H 321 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9081 (mp) REVERT: I 140 ARG cc_start: 0.9010 (ptp-110) cc_final: 0.8784 (mtp85) REVERT: I 321 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9072 (mp) REVERT: J 231 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8579 (mt) REVERT: J 321 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9120 (mp) REVERT: K 217 GLN cc_start: 0.8735 (mt0) cc_final: 0.8501 (mt0) REVERT: K 231 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8595 (mt) REVERT: K 321 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9168 (mp) REVERT: L 231 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8585 (mt) REVERT: L 245 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7290 (mmm-85) REVERT: L 321 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9085 (mp) REVERT: M 231 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8569 (mt) REVERT: N 320 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9002 (ttpt) outliers start: 171 outliers final: 97 residues processed: 586 average time/residue: 0.6311 time to fit residues: 446.5464 Evaluate side-chains 570 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 450 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 353 ASN Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 353 ASN Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 353 ASN Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 ARG Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 ARG Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 353 ASN Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 353 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 353 ASN Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 138 optimal weight: 6.9990 chunk 420 optimal weight: 4.9990 chunk 415 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 476 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 362 optimal weight: 6.9990 chunk 341 optimal weight: 0.9990 chunk 234 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 213 GLN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.102326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.069245 restraints weight = 56675.555| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.21 r_work: 0.2619 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9077 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 38906 Z= 0.214 Angle : 0.643 7.196 52962 Z= 0.340 Chirality : 0.048 0.195 6314 Planarity : 0.005 0.083 6958 Dihedral : 6.428 58.828 5451 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.04 % Allowed : 22.86 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.12), residues: 5012 helix: 2.84 (0.20), residues: 756 sheet: -0.10 (0.09), residues: 2632 loop : -0.78 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 105 TYR 0.011 0.002 TYR L 314 PHE 0.009 0.001 PHE C 200 TRP 0.009 0.001 TRP F 185 HIS 0.006 0.003 HIS A 123 Details of bonding type rmsd covalent geometry : bond 0.00517 (38906) covalent geometry : angle 0.64274 (52962) hydrogen bonds : bond 0.04846 ( 1372) hydrogen bonds : angle 5.08756 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 446 time to evaluate : 1.441 Fit side-chains REVERT: A 102 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: A 199 ASP cc_start: 0.8464 (m-30) cc_final: 0.8179 (m-30) REVERT: A 231 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8642 (mt) REVERT: A 245 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7396 (mmm-85) REVERT: A 321 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9075 (mp) REVERT: B 140 ARG cc_start: 0.9016 (ptp-110) cc_final: 0.8784 (mtp85) REVERT: B 321 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9069 (mp) REVERT: C 231 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8572 (mt) REVERT: C 321 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9102 (mp) REVERT: D 231 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8620 (mt) REVERT: D 321 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9133 (mp) REVERT: E 231 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8572 (mt) REVERT: E 245 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7338 (mmm-85) REVERT: E 321 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9085 (mp) REVERT: F 231 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8599 (mt) REVERT: H 199 ASP cc_start: 0.8469 (m-30) cc_final: 0.8177 (m-30) REVERT: H 231 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8638 (mt) REVERT: H 245 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7383 (mmm-85) REVERT: H 321 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9077 (mp) REVERT: I 140 ARG cc_start: 0.9009 (ptp-110) cc_final: 0.8777 (mtp85) REVERT: I 321 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9073 (mp) REVERT: J 102 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8464 (tp30) REVERT: J 231 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8573 (mt) REVERT: J 321 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9108 (mp) REVERT: K 231 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8623 (mt) REVERT: K 321 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9138 (mp) REVERT: L 231 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8572 (mt) REVERT: L 245 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7340 (mmm-85) REVERT: L 321 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9085 (mp) REVERT: M 102 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: M 231 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8595 (mt) outliers start: 169 outliers final: 95 residues processed: 575 average time/residue: 0.6349 time to fit residues: 441.4561 Evaluate side-chains 569 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 447 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 154 THR Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 245 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 370 ASN Chi-restraints excluded: chain H residue 418 ASP Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 363 ARG Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 356 optimal weight: 3.9990 chunk 224 optimal weight: 0.0030 chunk 382 optimal weight: 3.9990 chunk 497 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 443 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 476 optimal weight: 2.9990 overall best weight: 2.0154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.070416 restraints weight = 56874.124| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 2.21 r_work: 0.2642 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 38906 Z= 0.145 Angle : 0.599 7.056 52962 Z= 0.316 Chirality : 0.046 0.179 6314 Planarity : 0.005 0.087 6958 Dihedral : 6.264 58.290 5451 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.39 % Allowed : 23.34 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.12), residues: 5012 helix: 3.02 (0.20), residues: 756 sheet: -0.05 (0.10), residues: 2576 loop : -0.56 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG L 105 TYR 0.008 0.001 TYR L 314 PHE 0.008 0.001 PHE C 200 TRP 0.007 0.001 TRP M 185 HIS 0.005 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00348 (38906) covalent geometry : angle 0.59941 (52962) hydrogen bonds : bond 0.04246 ( 1372) hydrogen bonds : angle 4.94949 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 449 time to evaluate : 1.594 Fit side-chains REVERT: A 321 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9110 (mp) REVERT: B 140 ARG cc_start: 0.8994 (ptp-110) cc_final: 0.8785 (mtp85) REVERT: B 231 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8729 (mt) REVERT: B 321 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9090 (mp) REVERT: C 102 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8488 (tp30) REVERT: C 231 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 321 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9111 (mp) REVERT: D 231 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8621 (mt) REVERT: D 321 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9158 (mp) REVERT: E 231 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8573 (mt) REVERT: E 245 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6732 (mmm-85) REVERT: E 321 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9078 (mp) REVERT: F 231 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8564 (mt) REVERT: G 320 LYS cc_start: 0.9298 (ttmt) cc_final: 0.9011 (ttpt) REVERT: H 231 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8646 (mt) REVERT: H 321 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9107 (mp) REVERT: I 140 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8761 (mtp85) REVERT: I 231 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8738 (mt) REVERT: I 321 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9093 (mp) REVERT: J 231 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8574 (mt) REVERT: J 321 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9116 (mp) REVERT: K 217 GLN cc_start: 0.8746 (mt0) cc_final: 0.8500 (mt0) REVERT: K 231 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8623 (mt) REVERT: K 321 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9157 (mp) REVERT: L 231 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8575 (mt) REVERT: L 245 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6732 (mmm-85) REVERT: L 321 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9079 (mp) REVERT: M 231 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8566 (mt) REVERT: N 320 LYS cc_start: 0.9297 (ttmt) cc_final: 0.9007 (ttpt) outliers start: 142 outliers final: 96 residues processed: 562 average time/residue: 0.6671 time to fit residues: 450.1748 Evaluate side-chains 568 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 448 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 245 ARG Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 ARG Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 363 ARG Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 ARG Chi-restraints excluded: chain H residue 370 ASN Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 154 THR Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 353 ASN Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 154 THR Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 245 ARG Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 154 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 311 ASN Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 363 ARG Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 363 ARG Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 6 optimal weight: 1.9990 chunk 378 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 337 optimal weight: 0.0980 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 385 optimal weight: 6.9990 chunk 466 optimal weight: 6.9990 chunk 338 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.070975 restraints weight = 56445.605| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.21 r_work: 0.2654 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 38906 Z= 0.127 Angle : 0.586 7.182 52962 Z= 0.307 Chirality : 0.046 0.172 6314 Planarity : 0.005 0.089 6958 Dihedral : 6.084 57.789 5441 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.39 % Allowed : 23.34 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 5012 helix: 3.10 (0.20), residues: 756 sheet: -0.04 (0.10), residues: 2576 loop : -0.50 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG L 105 TYR 0.008 0.001 TYR M 314 PHE 0.007 0.001 PHE C 200 TRP 0.007 0.001 TRP M 185 HIS 0.005 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00303 (38906) covalent geometry : angle 0.58561 (52962) hydrogen bonds : bond 0.04019 ( 1372) hydrogen bonds : angle 4.87305 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10024 Ramachandran restraints generated. 5012 Oldfield, 0 Emsley, 5012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 454 time to evaluate : 1.022 Fit side-chains REVERT: A 245 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7525 (mmm-85) REVERT: A 321 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9096 (mp) REVERT: B 231 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8722 (mt) REVERT: B 321 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9071 (mp) REVERT: C 102 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8479 (tp30) REVERT: C 231 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8560 (mt) REVERT: D 102 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8337 (tp30) REVERT: D 140 ARG cc_start: 0.8943 (ptp-110) cc_final: 0.8577 (mtm180) REVERT: D 231 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8568 (mt) REVERT: D 321 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9139 (mp) REVERT: E 231 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8547 (mt) REVERT: E 321 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9104 (mp) REVERT: F 231 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8540 (mt) REVERT: G 320 LYS cc_start: 0.9296 (ttmt) cc_final: 0.9010 (ttpt) REVERT: H 321 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9097 (mp) REVERT: I 231 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8735 (mt) REVERT: I 321 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9072 (mp) REVERT: J 231 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8558 (mt) REVERT: K 105 ARG cc_start: 0.9099 (ttm110) cc_final: 0.8739 (ttm110) REVERT: K 140 ARG cc_start: 0.8960 (ptp-110) cc_final: 0.8585 (mtm180) REVERT: K 217 GLN cc_start: 0.8745 (mt0) cc_final: 0.8498 (mt0) REVERT: K 231 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8571 (mt) REVERT: K 321 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9149 (mp) REVERT: L 231 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8546 (mt) REVERT: L 321 LEU cc_start: 0.9484 (OUTLIER) cc_final: 0.9105 (mp) REVERT: M 231 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8540 (mt) REVERT: N 320 LYS cc_start: 0.9298 (ttmt) cc_final: 0.9010 (ttpt) outliers start: 142 outliers final: 86 residues processed: 567 average time/residue: 0.6671 time to fit residues: 455.3006 Evaluate side-chains 557 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 353 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 ARG Chi-restraints excluded: chain A residue 444 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 353 ASN Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 444 GLU Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 444 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 343 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 ARG Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 444 GLU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 363 ARG Chi-restraints excluded: chain F residue 444 GLU Chi-restraints excluded: chain G residue 119 VAL Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 353 ASN Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 444 GLU Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 353 ASN Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 363 ARG Chi-restraints excluded: chain H residue 444 GLU Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 231 LEU Chi-restraints excluded: chain I residue 274 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 353 ASN Chi-restraints excluded: chain I residue 362 THR Chi-restraints excluded: chain I residue 444 GLU Chi-restraints excluded: chain I residue 457 SER Chi-restraints excluded: chain J residue 154 THR Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain J residue 274 LEU Chi-restraints excluded: chain J residue 343 ASP Chi-restraints excluded: chain J residue 362 THR Chi-restraints excluded: chain J residue 433 LEU Chi-restraints excluded: chain J residue 444 GLU Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain K residue 177 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 THR Chi-restraints excluded: chain K residue 363 ARG Chi-restraints excluded: chain K residue 418 ASP Chi-restraints excluded: chain K residue 444 GLU Chi-restraints excluded: chain L residue 119 VAL Chi-restraints excluded: chain L residue 177 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 274 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 444 GLU Chi-restraints excluded: chain M residue 231 LEU Chi-restraints excluded: chain M residue 362 THR Chi-restraints excluded: chain M residue 363 ARG Chi-restraints excluded: chain M residue 444 GLU Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 154 THR Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 274 LEU Chi-restraints excluded: chain N residue 353 ASN Chi-restraints excluded: chain N residue 362 THR Chi-restraints excluded: chain N residue 444 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 385 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 74 optimal weight: 0.0070 chunk 227 optimal weight: 8.9990 chunk 143 optimal weight: 0.1980 chunk 450 optimal weight: 10.0000 chunk 475 optimal weight: 0.9980 chunk 466 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 382 optimal weight: 7.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN B 370 ASN C 370 ASN D 370 ASN E 370 ASN F 370 ASN G 370 ASN H 370 ASN I 370 ASN J 370 ASN K 370 ASN L 370 ASN M 370 ASN N 370 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.071009 restraints weight = 56727.330| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.21 r_work: 0.2654 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 38906 Z= 0.126 Angle : 0.681 61.599 52962 Z= 0.347 Chirality : 0.046 0.171 6314 Planarity : 0.005 0.085 6958 Dihedral : 5.992 57.823 5430 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.01 % Allowed : 23.91 % Favored : 73.08 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.12), residues: 5012 helix: 3.11 (0.20), residues: 756 sheet: -0.04 (0.10), residues: 2576 loop : -0.50 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 105 TYR 0.008 0.001 TYR M 314 PHE 0.007 0.001 PHE G 200 TRP 0.007 0.001 TRP M 185 HIS 0.005 0.002 HIS J 123 Details of bonding type rmsd covalent geometry : bond 0.00293 (38906) covalent geometry : angle 0.68145 (52962) hydrogen bonds : bond 0.03973 ( 1372) hydrogen bonds : angle 4.87208 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15873.42 seconds wall clock time: 269 minutes 27.15 seconds (16167.15 seconds total)