Starting phenix.real_space_refine on Thu Sep 18 19:22:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivq_60932/09_2025/9ivq_60932.cif" } resolution = 2.66 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= 0.010 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 89 5.16 5 C 12487 2.51 5 N 3497 2.21 5 O 3685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "P" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "N" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "M" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "O" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "V" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "T" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "R" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "Q" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "S" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "X" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "E" Number of atoms: 1088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} bond proxies already assigned to first conformer: 1101 Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "H" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "F" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "J" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "K" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "W" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 296 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS E 73 " occ=0.45 ... (10 atoms not shown) pdb=" SG BCYS E 73 " occ=0.55 Time building chain proxies: 4.91, per 1000 atoms: 0.25 Number of scatterers: 19758 At special positions: 0 Unit cell: (112.375, 100.05, 128.325, 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 89 16.00 O 3685 8.00 N 3497 7.00 C 12487 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: 1.46 Conformation dependent library (CDL) restraints added in 794.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 32 sheets defined 33.4% alpha, 42.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 7 through 26 removed outlier: 3.752A pdb=" N ASN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.285A pdb=" N HIS A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'C' and resid 7 through 26 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.183A pdb=" N HIS C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'D' and resid 7 through 26 removed outlier: 3.614A pdb=" N ASN D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 4.654A pdb=" N HIS D 31 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'B' and resid 7 through 26 removed outlier: 4.243A pdb=" N ASN B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 32 removed outlier: 4.795A pdb=" N HIS B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 69 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'L' and resid 481 through 486 Processing helix chain 'L' and resid 499 through 508 removed outlier: 3.561A pdb=" N SER L 507 " --> pdb=" O ASP L 503 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP L 508 " --> pdb=" O LEU L 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 26 Processing helix chain 'P' and resid 27 through 33 removed outlier: 4.495A pdb=" N HIS P 31 " --> pdb=" O ASP P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 69 Processing helix chain 'P' and resid 86 through 88 No H-bonds generated for 'chain 'P' and resid 86 through 88' Processing helix chain 'P' and resid 100 through 103 Processing helix chain 'N' and resid 7 through 26 Processing helix chain 'N' and resid 27 through 32 removed outlier: 3.923A pdb=" N HIS N 31 " --> pdb=" O ASP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 69 removed outlier: 3.531A pdb=" N ASN N 69 " --> pdb=" O VAL N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'M' and resid 7 through 26 Processing helix chain 'M' and resid 27 through 32 removed outlier: 4.678A pdb=" N HIS M 31 " --> pdb=" O ASP M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 68 Processing helix chain 'O' and resid 7 through 26 Processing helix chain 'O' and resid 27 through 32 removed outlier: 4.776A pdb=" N HIS O 31 " --> pdb=" O ASP O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 69 removed outlier: 3.644A pdb=" N ASN O 69 " --> pdb=" O VAL O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 88 No H-bonds generated for 'chain 'O' and resid 86 through 88' Processing helix chain 'O' and resid 134 through 138 Processing helix chain 'V' and resid 481 through 487 removed outlier: 3.506A pdb=" N SER V 487 " --> pdb=" O ILE V 483 " (cutoff:3.500A) Processing helix chain 'V' and resid 499 through 506 Processing helix chain 'T' and resid 7 through 26 removed outlier: 3.798A pdb=" N ASN T 24 " --> pdb=" O TYR T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 34 removed outlier: 4.401A pdb=" N HIS T 31 " --> pdb=" O ASP T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 68 Processing helix chain 'T' and resid 86 through 88 No H-bonds generated for 'chain 'T' and resid 86 through 88' Processing helix chain 'R' and resid 7 through 26 removed outlier: 3.662A pdb=" N ASN R 24 " --> pdb=" O TYR R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 32 removed outlier: 4.029A pdb=" N HIS R 31 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 69 Processing helix chain 'R' and resid 86 through 88 No H-bonds generated for 'chain 'R' and resid 86 through 88' Processing helix chain 'Q' and resid 7 through 26 removed outlier: 3.824A pdb=" N ASN Q 24 " --> pdb=" O TYR Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 32 removed outlier: 4.789A pdb=" N HIS Q 31 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 69 Processing helix chain 'Q' and resid 86 through 88 No H-bonds generated for 'chain 'Q' and resid 86 through 88' Processing helix chain 'Q' and resid 135 through 137 No H-bonds generated for 'chain 'Q' and resid 135 through 137' Processing helix chain 'S' and resid 7 through 26 removed outlier: 4.241A pdb=" N ASN S 24 " --> pdb=" O TYR S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 removed outlier: 4.716A pdb=" N HIS S 31 " --> pdb=" O ASP S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 69 removed outlier: 3.653A pdb=" N ASN S 69 " --> pdb=" O VAL S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 86 through 88 No H-bonds generated for 'chain 'S' and resid 86 through 88' Processing helix chain 'S' and resid 135 through 137 No H-bonds generated for 'chain 'S' and resid 135 through 137' Processing helix chain 'X' and resid 481 through 486 Processing helix chain 'X' and resid 499 through 507 removed outlier: 4.830A pdb=" N SER X 507 " --> pdb=" O ASP X 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.756A pdb=" N ASN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.509A pdb=" N HIS E 31 " --> pdb=" O ASP E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 69 removed outlier: 3.545A pdb=" N ASN E 69 " --> pdb=" O VAL E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'G' and resid 7 through 26 Processing helix chain 'G' and resid 27 through 32 removed outlier: 4.033A pdb=" N HIS G 31 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 86 through 88 No H-bonds generated for 'chain 'G' and resid 86 through 88' Processing helix chain 'H' and resid 7 through 26 Processing helix chain 'H' and resid 27 through 32 removed outlier: 5.140A pdb=" N HIS H 31 " --> pdb=" O ASP H 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 32 " --> pdb=" O MET H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 69 Processing helix chain 'F' and resid 7 through 26 Processing helix chain 'F' and resid 27 through 32 removed outlier: 4.731A pdb=" N HIS F 31 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 69 removed outlier: 3.631A pdb=" N ASN F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 134 through 138 Processing helix chain 'J' and resid 483 through 487 Processing helix chain 'J' and resid 499 through 508 removed outlier: 3.763A pdb=" N SER J 507 " --> pdb=" O ASP J 503 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP J 508 " --> pdb=" O LEU J 504 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 488 Processing helix chain 'K' and resid 500 through 508 removed outlier: 3.858A pdb=" N LEU K 504 " --> pdb=" O GLU K 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR K 505 " --> pdb=" O VAL K 501 " (cutoff:3.500A) Processing helix chain 'W' and resid 481 through 488 Processing helix chain 'W' and resid 500 through 508 removed outlier: 3.928A pdb=" N LEU W 504 " --> pdb=" O GLU W 500 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR W 505 " --> pdb=" O VAL W 501 " (cutoff:3.500A) Processing helix chain 'U' and resid 481 through 488 Processing helix chain 'U' and resid 500 through 508 removed outlier: 3.869A pdb=" N LEU U 504 " --> pdb=" O GLU U 500 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR U 505 " --> pdb=" O VAL U 501 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP U 508 " --> pdb=" O LEU U 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 481 through 488 Processing helix chain 'I' and resid 500 through 508 removed outlier: 3.931A pdb=" N LEU I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR I 505 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 508 " --> pdb=" O LEU I 504 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 removed outlier: 11.019A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS A 127 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL A 126 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA A 115 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU A 97 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ILE A 77 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 11.019A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N HIS A 127 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 55 through 56 removed outlier: 10.973A pdb=" N GLY C 35 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N TYR C 125 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N ASN C 37 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 127 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VAL C 126 " --> pdb=" O ALA C 115 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA C 115 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU C 97 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE C 77 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N SER C 99 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR C 75 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 56 removed outlier: 10.973A pdb=" N GLY C 35 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 9.613A pdb=" N TYR C 125 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N ASN C 37 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS C 127 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 56 removed outlier: 10.992A pdb=" N GLY D 35 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N TYR D 125 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N ASN D 37 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS D 127 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL D 126 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 115 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 91 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 82 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN D 93 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 80 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET D 95 " --> pdb=" O ARG D 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 56 removed outlier: 10.992A pdb=" N GLY D 35 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N TYR D 125 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 10.489A pdb=" N ASN D 37 " --> pdb=" O TYR D 125 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N HIS D 127 " --> pdb=" O ASN D 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 removed outlier: 11.156A pdb=" N GLY B 35 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N TYR B 125 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N ASN B 37 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 127 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N VAL B 126 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA B 115 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 91 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 82 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 93 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL B 80 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET B 95 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 55 through 56 removed outlier: 11.156A pdb=" N GLY B 35 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N TYR B 125 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N ASN B 37 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS B 127 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 474 through 475 removed outlier: 6.725A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) removed outlier: 10.943A pdb=" N GLY H 35 " --> pdb=" O LYS H 123 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N TYR H 125 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N ASN H 37 " --> pdb=" O TYR H 125 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS H 127 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 474 through 475 removed outlier: 6.725A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL H 126 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA H 115 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU H 97 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE H 77 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N SER H 99 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR H 75 " --> pdb=" O SER H 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 55 through 56 removed outlier: 5.578A pdb=" N VAL P 126 " --> pdb=" O ALA P 115 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA P 115 " --> pdb=" O VAL P 126 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU P 97 " --> pdb=" O ILE P 77 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ILE P 77 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N SER P 99 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR P 75 " --> pdb=" O SER P 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'N' and resid 34 through 42 removed outlier: 11.001A pdb=" N GLY N 35 " --> pdb=" O LYS N 123 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N TYR N 125 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN N 37 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS N 127 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL N 126 " --> pdb=" O ALA N 115 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA N 115 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL N 91 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA N 82 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN N 93 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL N 80 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET N 95 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 34 through 42 removed outlier: 11.001A pdb=" N GLY N 35 " --> pdb=" O LYS N 123 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N TYR N 125 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N ASN N 37 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N HIS N 127 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 55 through 56 removed outlier: 10.939A pdb=" N GLY M 35 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N TYR M 125 " --> pdb=" O GLY M 35 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ASN M 37 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N HIS M 127 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VAL M 126 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA M 115 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU M 97 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE M 77 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER M 99 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR M 75 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 55 through 56 removed outlier: 10.939A pdb=" N GLY M 35 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N TYR M 125 " --> pdb=" O GLY M 35 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N ASN M 37 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N HIS M 127 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 55 through 56 removed outlier: 10.626A pdb=" N GLY O 35 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N TYR O 125 " --> pdb=" O GLY O 35 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N ASN O 37 " --> pdb=" O TYR O 125 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS O 127 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL O 126 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA O 115 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY O 89 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA O 84 " --> pdb=" O GLY O 89 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL O 91 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA O 82 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN O 93 " --> pdb=" O VAL O 80 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL O 80 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET O 95 " --> pdb=" O ARG O 78 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 55 through 56 removed outlier: 10.626A pdb=" N GLY O 35 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N TYR O 125 " --> pdb=" O GLY O 35 " (cutoff:3.500A) removed outlier: 9.473A pdb=" N ASN O 37 " --> pdb=" O TYR O 125 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS O 127 " --> pdb=" O ASN O 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 474 through 475 removed outlier: 6.848A pdb=" N THR V 474 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL Q 126 " --> pdb=" O THR V 474 " (cutoff:3.500A) removed outlier: 10.880A pdb=" N GLY Q 35 " --> pdb=" O LYS Q 123 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N TYR Q 125 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) removed outlier: 9.453A pdb=" N ASN Q 37 " --> pdb=" O TYR Q 125 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS Q 127 " --> pdb=" O ASN Q 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 474 through 475 removed outlier: 6.848A pdb=" N THR V 474 " --> pdb=" O PHE Q 124 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N VAL Q 126 " --> pdb=" O THR V 474 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA Q 115 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ILE Q 77 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N SER Q 99 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N THR Q 75 " --> pdb=" O SER Q 99 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 55 through 56 removed outlier: 4.166A pdb=" N GLY T 43 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR T 133 " --> pdb=" O GLY T 43 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL T 126 " --> pdb=" O ALA T 115 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA T 115 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU T 97 " --> pdb=" O ILE T 77 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE T 77 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER T 99 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR T 75 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 55 through 56 removed outlier: 4.166A pdb=" N GLY T 43 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TYR T 133 " --> pdb=" O GLY T 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 34 through 42 removed outlier: 11.079A pdb=" N GLY R 35 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N TYR R 125 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASN R 37 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS R 127 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL R 126 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA R 115 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU R 97 " --> pdb=" O ILE R 77 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE R 77 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER R 99 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR R 75 " --> pdb=" O SER R 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 34 through 42 removed outlier: 11.079A pdb=" N GLY R 35 " --> pdb=" O LYS R 123 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N TYR R 125 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASN R 37 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS R 127 " --> pdb=" O ASN R 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 55 through 56 removed outlier: 10.606A pdb=" N GLY S 35 " --> pdb=" O LYS S 123 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N TYR S 125 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ASN S 37 " --> pdb=" O TYR S 125 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N HIS S 127 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL S 126 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA S 115 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL S 91 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA S 82 " --> pdb=" O VAL S 91 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN S 93 " --> pdb=" O VAL S 80 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL S 80 " --> pdb=" O GLN S 93 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N MET S 95 " --> pdb=" O ARG S 78 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 55 through 56 removed outlier: 10.606A pdb=" N GLY S 35 " --> pdb=" O LYS S 123 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N TYR S 125 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ASN S 37 " --> pdb=" O TYR S 125 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N HIS S 127 " --> pdb=" O ASN S 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 55 through 56 removed outlier: 5.522A pdb=" N VAL E 126 " --> pdb=" O ALA E 115 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 115 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU E 97 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE E 77 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER E 99 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR E 75 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AD2, first strand: chain 'G' and resid 55 through 56 removed outlier: 11.027A pdb=" N GLY G 35 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N TYR G 125 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ASN G 37 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS G 127 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL G 126 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA G 115 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU G 97 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE G 77 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N SER G 99 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR G 75 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 55 through 56 removed outlier: 11.027A pdb=" N GLY G 35 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N TYR G 125 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ASN G 37 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N HIS G 127 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 55 through 56 removed outlier: 11.087A pdb=" N GLY F 35 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR F 125 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASN F 37 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS F 127 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL F 126 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA F 115 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU F 97 " --> pdb=" O ILE F 77 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ILE F 77 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N SER F 99 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N THR F 75 " --> pdb=" O SER F 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 55 through 56 removed outlier: 11.087A pdb=" N GLY F 35 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR F 125 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 9.507A pdb=" N ASN F 37 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N HIS F 127 " --> pdb=" O ASN F 37 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5813 1.33 - 1.46: 4042 1.46 - 1.58: 10206 1.58 - 1.70: 1 1.70 - 1.82: 161 Bond restraints: 20223 Sorted by residual: bond pdb=" N VAL P 137 " pdb=" CA VAL P 137 " ideal model delta sigma weight residual 1.459 1.497 -0.038 9.10e-03 1.21e+04 1.77e+01 bond pdb=" C LYS D 50 " pdb=" N PRO D 51 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" N GLN R 103 " pdb=" CA GLN R 103 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.84e+00 bond pdb=" N VAL O 120 " pdb=" CA VAL O 120 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.71e+00 bond pdb=" N ILE R 61 " pdb=" CA ILE R 61 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.46e+00 ... (remaining 20218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 26207 2.22 - 4.44: 1034 4.44 - 6.66: 84 6.66 - 8.89: 18 8.89 - 11.11: 8 Bond angle restraints: 27351 Sorted by residual: angle pdb=" N ILE C 61 " pdb=" CA ILE C 61 " pdb=" C ILE C 61 " ideal model delta sigma weight residual 110.72 104.49 6.23 1.01e+00 9.80e-01 3.81e+01 angle pdb=" CB GLN E 134 " pdb=" CG GLN E 134 " pdb=" CD GLN E 134 " ideal model delta sigma weight residual 112.60 102.34 10.26 1.70e+00 3.46e-01 3.64e+01 angle pdb=" CB GLN A 134 " pdb=" CG GLN A 134 " pdb=" CD GLN A 134 " ideal model delta sigma weight residual 112.60 103.91 8.69 1.70e+00 3.46e-01 2.61e+01 angle pdb=" CA GLY D 44 " pdb=" C GLY D 44 " pdb=" O GLY D 44 " ideal model delta sigma weight residual 122.29 118.19 4.10 8.10e-01 1.52e+00 2.56e+01 angle pdb=" N ASP D 46 " pdb=" CA ASP D 46 " pdb=" C ASP D 46 " ideal model delta sigma weight residual 111.36 106.39 4.97 1.09e+00 8.42e-01 2.08e+01 ... (remaining 27346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 10395 18.04 - 36.07: 1237 36.07 - 54.11: 277 54.11 - 72.14: 39 72.14 - 90.18: 5 Dihedral angle restraints: 11953 sinusoidal: 4833 harmonic: 7120 Sorted by residual: dihedral pdb=" CA ASN C 102 " pdb=" C ASN C 102 " pdb=" N GLN C 103 " pdb=" CA GLN C 103 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASN G 102 " pdb=" C ASN G 102 " pdb=" N GLN G 103 " pdb=" CA GLN G 103 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" C GLN E 134 " pdb=" N GLN E 134 " pdb=" CA GLN E 134 " pdb=" CB GLN E 134 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 11950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2281 0.066 - 0.131: 521 0.131 - 0.196: 78 0.196 - 0.262: 19 0.262 - 0.327: 6 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA LEU A 97 " pdb=" N LEU A 97 " pdb=" C LEU A 97 " pdb=" CB LEU A 97 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ILE C 61 " pdb=" N ILE C 61 " pdb=" C ILE C 61 " pdb=" CB ILE C 61 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA GLN M 134 " pdb=" N GLN M 134 " pdb=" C GLN M 134 " pdb=" CB GLN M 134 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2902 not shown) Planarity restraints: 3638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 133 " -0.014 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C TYR A 133 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 133 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN A 134 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 88 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" CG ASP C 88 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP C 88 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP C 88 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 26 " -0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO G 27 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO G 27 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 27 " -0.034 5.00e-02 4.00e+02 ... (remaining 3635 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1051 2.73 - 3.27: 19855 3.27 - 3.81: 32960 3.81 - 4.36: 41544 4.36 - 4.90: 71578 Nonbonded interactions: 166988 Sorted by model distance: nonbonded pdb=" OG SER P 47 " pdb=" OD1 ASN P 48 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR F 20 " pdb=" OE1 GLN F 110 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR C 20 " pdb=" OE1 GLN C 110 " model vdw 2.205 3.040 nonbonded pdb=" OE2 GLU H 117 " pdb=" OG SER H 119 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR G 20 " pdb=" OE1 GLN G 110 " model vdw 2.224 3.040 ... (remaining 166983 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'B' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'C' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'D' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'E' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'F' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'G' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'H' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'M' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'N' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'O' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'P' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'Q' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'R' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'S' and (resid 5 through 72 or resid 74 through 138)) selection = (chain 'T' and (resid 5 through 72 or resid 74 through 138)) } ncs_group { reference = (chain 'I' and resid 472 through 508) selection = chain 'J' selection = (chain 'K' and resid 472 through 508) selection = chain 'L' selection = (chain 'U' and resid 472 through 508) selection = chain 'V' selection = (chain 'W' and resid 472 through 508) selection = chain 'X' } 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=0.45 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.250 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 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 : 0.006 0.092 20223 Z= 0.376 Angle : 0.886 11.107 27351 Z= 0.574 Chirality : 0.059 0.327 2905 Planarity : 0.004 0.061 3638 Dihedral : 15.696 90.176 7383 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.23 % Allowed : 26.84 % Favored : 70.93 % Cbeta Deviations : 0.04 % 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: 1.10 (0.18), residues: 2415 helix: 1.92 (0.21), residues: 610 sheet: 0.23 (0.19), residues: 650 loop : 0.52 (0.21), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 63 TYR 0.015 0.001 TYR H 133 PHE 0.015 0.002 PHE O 15 TRP 0.001 0.000 TRP U 509 HIS 0.007 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00555 (20223) covalent geometry : angle 0.88565 (27351) hydrogen bonds : bond 0.10761 ( 930) hydrogen bonds : angle 5.70339 ( 2691) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 681 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8867 (mmpt) REVERT: C 14 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7983 (tm-30) REVERT: C 72 ASN cc_start: 0.8279 (t0) cc_final: 0.7789 (t0) REVERT: D 14 GLU cc_start: 0.8821 (tp30) cc_final: 0.8611 (tp30) REVERT: D 66 MET cc_start: 0.8793 (mmm) cc_final: 0.8538 (mmm) REVERT: D 136 GLU cc_start: 0.8197 (tt0) cc_final: 0.7953 (tt0) REVERT: B 13 ARG cc_start: 0.8272 (ttm-80) cc_final: 0.7556 (mmt90) REVERT: B 50 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8349 (pptt) REVERT: L 502 ASP cc_start: 0.8980 (m-30) cc_final: 0.8736 (m-30) REVERT: N 14 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7948 (tm-30) REVERT: N 62 HIS cc_start: 0.8847 (t-90) cc_final: 0.8269 (t-90) REVERT: N 76 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8025 (mttm) REVERT: N 103 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8477 (mm-40) REVERT: M 135 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8176 (p0) REVERT: O 37 ASN cc_start: 0.8553 (m-40) cc_final: 0.8085 (p0) REVERT: O 59 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8769 (mmmm) REVERT: O 87 ASN cc_start: 0.9419 (m-40) cc_final: 0.9208 (m-40) REVERT: T 66 MET cc_start: 0.9353 (mmm) cc_final: 0.9149 (mmm) REVERT: T 87 ASN cc_start: 0.9209 (m-40) cc_final: 0.8889 (m-40) REVERT: R 72 ASN cc_start: 0.8070 (t0) cc_final: 0.7529 (t0) REVERT: R 102 ASN cc_start: 0.8836 (m110) cc_final: 0.8584 (m110) REVERT: R 103 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8553 (mp10) REVERT: Q 17 ARG cc_start: 0.8829 (ttp80) cc_final: 0.8331 (ttp80) REVERT: S 50 LYS cc_start: 0.8594 (pttm) cc_final: 0.8307 (pptt) REVERT: S 87 ASN cc_start: 0.9212 (m-40) cc_final: 0.8973 (m110) REVERT: X 479 ASN cc_start: 0.8728 (m-40) cc_final: 0.8491 (m-40) REVERT: X 484 GLU cc_start: 0.8984 (mp0) cc_final: 0.8725 (mp0) REVERT: E 68 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8735 (mm-40) REVERT: H 14 GLU cc_start: 0.8840 (tp30) cc_final: 0.8217 (tp30) REVERT: F 68 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: F 123 LYS cc_start: 0.8980 (tttp) cc_final: 0.8644 (tttp) outliers start: 48 outliers final: 28 residues processed: 710 average time/residue: 0.6216 time to fit residues: 493.9270 Evaluate side-chains 648 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 618 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 492 THR Chi-restraints excluded: chain P residue 73 CYS Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 135 ASP Chi-restraints excluded: chain O residue 47 SER Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 50 LYS Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain X residue 492 THR Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain U residue 483 ILE Chi-restraints excluded: chain I residue 474 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 87 ASN C 48 ASN C 58 GLN C 62 HIS C 68 GLN C 101 ASN D 58 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 110 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 ASN T 68 GLN T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN R 101 ASN R 110 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 25 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.069860 restraints weight = 43631.115| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.03 r_work: 0.2716 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20223 Z= 0.211 Angle : 0.617 7.461 27351 Z= 0.323 Chirality : 0.046 0.173 2905 Planarity : 0.004 0.045 3638 Dihedral : 5.043 52.469 2733 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.52 % Allowed : 25.27 % Favored : 69.22 % 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: 1.50 (0.18), residues: 2415 helix: 2.39 (0.21), residues: 610 sheet: 0.04 (0.18), residues: 722 loop : 1.08 (0.23), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 17 TYR 0.016 0.002 TYR F 20 PHE 0.019 0.002 PHE H 15 TRP 0.005 0.001 TRP K 509 HIS 0.008 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00487 (20223) covalent geometry : angle 0.61725 (27351) hydrogen bonds : bond 0.03834 ( 930) hydrogen bonds : angle 4.99719 ( 2691) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 634 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9239 (ttmt) cc_final: 0.8930 (mmtm) REVERT: A 87 ASN cc_start: 0.9164 (m-40) cc_final: 0.8772 (m110) REVERT: C 14 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8172 (tm-30) REVERT: C 63 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8842 (ttp80) REVERT: C 72 ASN cc_start: 0.8395 (t0) cc_final: 0.7731 (t0) REVERT: C 88 ASP cc_start: 0.8396 (t0) cc_final: 0.8078 (t0) REVERT: C 103 GLN cc_start: 0.9041 (mp10) cc_final: 0.8611 (mp10) REVERT: C 117 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 14 GLU cc_start: 0.9000 (tp30) cc_final: 0.8679 (tp30) REVERT: D 25 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: D 66 MET cc_start: 0.8747 (mmm) cc_final: 0.8543 (mmm) REVERT: B 50 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8271 (pptt) REVERT: N 14 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8157 (tm-30) REVERT: N 64 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8257 (tmtm) REVERT: N 88 ASP cc_start: 0.8545 (t0) cc_final: 0.8055 (t0) REVERT: N 103 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8657 (mm-40) REVERT: N 117 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8278 (tm-30) REVERT: M 14 GLU cc_start: 0.8811 (tp30) cc_final: 0.8370 (mm-30) REVERT: M 25 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: M 103 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: O 59 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8844 (mmmm) REVERT: T 87 ASN cc_start: 0.9250 (m-40) cc_final: 0.8898 (m-40) REVERT: T 103 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8483 (mm110) REVERT: R 14 GLU cc_start: 0.8837 (tp30) cc_final: 0.8118 (tm-30) REVERT: R 63 ARG cc_start: 0.9249 (mtp85) cc_final: 0.8946 (ttp80) REVERT: R 72 ASN cc_start: 0.8191 (t0) cc_final: 0.7645 (t0) REVERT: R 88 ASP cc_start: 0.8359 (t0) cc_final: 0.8108 (t0) REVERT: R 99 SER cc_start: 0.8283 (m) cc_final: 0.7887 (p) REVERT: R 102 ASN cc_start: 0.9038 (m110) cc_final: 0.8703 (m110) REVERT: R 103 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8743 (mm-40) REVERT: R 105 LEU cc_start: 0.8486 (mt) cc_final: 0.8075 (tp) REVERT: R 117 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8121 (tm-30) REVERT: Q 14 GLU cc_start: 0.8852 (tp30) cc_final: 0.8555 (mm-30) REVERT: Q 66 MET cc_start: 0.9074 (mmm) cc_final: 0.8847 (mmm) REVERT: Q 100 ASN cc_start: 0.7943 (t0) cc_final: 0.7584 (t0) REVERT: Q 103 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: S 50 LYS cc_start: 0.8472 (pttm) cc_final: 0.8192 (pptt) REVERT: S 63 ARG cc_start: 0.8818 (ttp-110) cc_final: 0.8560 (ttm110) REVERT: S 87 ASN cc_start: 0.9241 (m-40) cc_final: 0.8979 (m-40) REVERT: X 484 GLU cc_start: 0.8896 (mp0) cc_final: 0.8579 (mp0) REVERT: E 68 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8693 (mm-40) REVERT: E 103 GLN cc_start: 0.8609 (mt0) cc_final: 0.8394 (mm110) REVERT: E 117 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8436 (mm-30) REVERT: G 3 MET cc_start: 0.8573 (mmm) cc_final: 0.8315 (tpp) REVERT: G 25 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8725 (mm110) REVERT: G 62 HIS cc_start: 0.8843 (t70) cc_final: 0.8638 (t-90) REVERT: G 66 MET cc_start: 0.9409 (mmm) cc_final: 0.9183 (mmm) REVERT: G 87 ASN cc_start: 0.8652 (t0) cc_final: 0.8154 (t0) REVERT: G 103 GLN cc_start: 0.9121 (mp10) cc_final: 0.8814 (mp10) REVERT: H 14 GLU cc_start: 0.8900 (tp30) cc_final: 0.8365 (tp30) REVERT: H 103 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: H 134 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7574 (mm-40) REVERT: F 107 ARG cc_start: 0.8811 (mtt180) cc_final: 0.8600 (mtt180) REVERT: F 117 GLU cc_start: 0.8542 (pp20) cc_final: 0.8292 (pp20) REVERT: F 123 LYS cc_start: 0.9147 (tttp) cc_final: 0.8853 (ttmm) outliers start: 119 outliers final: 44 residues processed: 694 average time/residue: 0.6012 time to fit residues: 467.6566 Evaluate side-chains 641 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 589 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain X residue 486 LEU Chi-restraints excluded: chain X residue 497 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 25 GLN Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain W residue 477 ASP Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain I residue 505 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 36 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 213 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN A 87 ASN C 58 GLN C 68 GLN C 93 GLN D 58 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN B 68 GLN B 87 ASN P 68 GLN P 103 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN ** O 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 ASN S 68 GLN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.071541 restraints weight = 47800.548| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.12 r_work: 0.2743 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 0.049 20223 Z= 0.150 Angle : 0.602 7.416 27351 Z= 0.312 Chirality : 0.045 0.166 2905 Planarity : 0.003 0.038 3638 Dihedral : 4.611 51.994 2707 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.96 % Allowed : 26.75 % Favored : 68.29 % 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: 1.58 (0.18), residues: 2415 helix: 2.37 (0.20), residues: 624 sheet: 0.08 (0.18), residues: 722 loop : 1.17 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 17 TYR 0.015 0.001 TYR G 20 PHE 0.015 0.002 PHE R 131 TRP 0.001 0.000 TRP K 509 HIS 0.007 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00344 (20223) covalent geometry : angle 0.60162 (27351) hydrogen bonds : bond 0.03522 ( 930) hydrogen bonds : angle 4.85027 ( 2691) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 648 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9211 (ttmt) cc_final: 0.8896 (mmtm) REVERT: A 87 ASN cc_start: 0.9197 (m110) cc_final: 0.8753 (m110) REVERT: A 103 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8556 (mp10) REVERT: C 14 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 63 ARG cc_start: 0.9171 (ttm-80) cc_final: 0.8824 (ttp80) REVERT: C 71 THR cc_start: 0.9102 (m) cc_final: 0.8892 (p) REVERT: C 72 ASN cc_start: 0.8424 (t0) cc_final: 0.7717 (t0) REVERT: C 88 ASP cc_start: 0.8449 (t0) cc_final: 0.8043 (t0) REVERT: C 103 GLN cc_start: 0.9007 (mp10) cc_final: 0.8203 (mp10) REVERT: C 107 ARG cc_start: 0.8167 (mtp180) cc_final: 0.7889 (mtp180) REVERT: C 117 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7979 (tm-30) REVERT: D 25 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7998 (mt0) REVERT: D 66 MET cc_start: 0.8731 (mmm) cc_final: 0.8494 (mmm) REVERT: B 50 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8292 (pptt) REVERT: B 63 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8633 (ttm110) REVERT: N 14 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8095 (tm-30) REVERT: N 88 ASP cc_start: 0.8528 (t0) cc_final: 0.8026 (t0) REVERT: N 103 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8677 (mm-40) REVERT: N 117 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8119 (tm-30) REVERT: N 134 GLN cc_start: 0.8335 (mt0) cc_final: 0.8128 (mt0) REVERT: M 14 GLU cc_start: 0.8757 (tp30) cc_final: 0.8557 (tp30) REVERT: M 17 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8737 (ttp80) REVERT: M 25 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: M 59 LYS cc_start: 0.9141 (tttm) cc_final: 0.8920 (tttm) REVERT: M 103 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: M 117 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7639 (tm-30) REVERT: M 123 LYS cc_start: 0.8646 (tttp) cc_final: 0.8414 (tptt) REVERT: O 37 ASN cc_start: 0.8431 (m110) cc_final: 0.8008 (p0) REVERT: O 59 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8836 (mmmm) REVERT: O 60 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8656 (mm-30) REVERT: O 63 ARG cc_start: 0.8838 (ttp-110) cc_final: 0.8616 (ttm110) REVERT: T 87 ASN cc_start: 0.9232 (m-40) cc_final: 0.8975 (m110) REVERT: T 103 GLN cc_start: 0.8841 (mt0) cc_final: 0.8601 (mm110) REVERT: R 63 ARG cc_start: 0.9231 (mtp85) cc_final: 0.8935 (ttp80) REVERT: R 88 ASP cc_start: 0.8379 (t0) cc_final: 0.8035 (t0) REVERT: R 99 SER cc_start: 0.8317 (m) cc_final: 0.8008 (p) REVERT: R 103 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8521 (mp10) REVERT: R 117 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8024 (tm-30) REVERT: Q 14 GLU cc_start: 0.8771 (tp30) cc_final: 0.8485 (mm-30) REVERT: Q 25 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: Q 66 MET cc_start: 0.9065 (mmm) cc_final: 0.8859 (mmm) REVERT: Q 100 ASN cc_start: 0.7939 (t0) cc_final: 0.7626 (t0) REVERT: Q 103 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: S 50 LYS cc_start: 0.8441 (pttm) cc_final: 0.8166 (pptt) REVERT: S 63 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8537 (ttm110) REVERT: X 484 GLU cc_start: 0.8892 (mp0) cc_final: 0.8619 (mp0) REVERT: E 68 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8686 (mm-40) REVERT: E 103 GLN cc_start: 0.8605 (mt0) cc_final: 0.8375 (mm110) REVERT: G 3 MET cc_start: 0.8500 (mmm) cc_final: 0.8253 (tpp) REVERT: G 62 HIS cc_start: 0.8836 (t70) cc_final: 0.8577 (t-90) REVERT: G 66 MET cc_start: 0.9446 (mmm) cc_final: 0.9207 (mmm) REVERT: G 72 ASN cc_start: 0.8781 (t0) cc_final: 0.8141 (t0) REVERT: G 87 ASN cc_start: 0.8608 (t0) cc_final: 0.8083 (t0) REVERT: G 88 ASP cc_start: 0.8387 (t0) cc_final: 0.8117 (t0) REVERT: G 101 ASN cc_start: 0.8971 (m-40) cc_final: 0.8735 (m-40) REVERT: G 103 GLN cc_start: 0.9113 (mp10) cc_final: 0.8666 (mp10) REVERT: G 117 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7865 (tm-30) REVERT: H 14 GLU cc_start: 0.8874 (tp30) cc_final: 0.8325 (tp30) REVERT: H 103 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: H 134 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7740 (mm-40) REVERT: F 50 LYS cc_start: 0.8664 (pptt) cc_final: 0.8464 (pmtt) REVERT: F 117 GLU cc_start: 0.8521 (pp20) cc_final: 0.8306 (pp20) REVERT: F 123 LYS cc_start: 0.9114 (tttp) cc_final: 0.8826 (ttmm) outliers start: 107 outliers final: 56 residues processed: 709 average time/residue: 0.6167 time to fit residues: 490.3869 Evaluate side-chains 662 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 600 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 502 ASP Chi-restraints excluded: chain U residue 505 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 165 optimal weight: 0.7980 chunk 196 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN C 58 GLN C 68 GLN D 58 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 103 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 69 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.098447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.068433 restraints weight = 54760.442| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.39 r_work: 0.2683 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20223 Z= 0.210 Angle : 0.622 9.819 27351 Z= 0.321 Chirality : 0.046 0.173 2905 Planarity : 0.004 0.038 3638 Dihedral : 4.638 44.070 2706 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.33 % Allowed : 27.54 % Favored : 67.13 % 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: 1.55 (0.18), residues: 2415 helix: 2.17 (0.20), residues: 644 sheet: 0.13 (0.19), residues: 714 loop : 1.19 (0.23), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 13 TYR 0.017 0.001 TYR F 20 PHE 0.018 0.002 PHE H 15 TRP 0.002 0.000 TRP K 509 HIS 0.007 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00488 (20223) covalent geometry : angle 0.62239 (27351) hydrogen bonds : bond 0.03707 ( 930) hydrogen bonds : angle 4.86796 ( 2691) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 631 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9235 (ttmt) cc_final: 0.8896 (mmtm) REVERT: A 87 ASN cc_start: 0.9171 (m110) cc_final: 0.8607 (m110) REVERT: A 134 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: C 14 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 63 ARG cc_start: 0.9180 (ttm-80) cc_final: 0.8840 (ttp80) REVERT: C 71 THR cc_start: 0.9091 (m) cc_final: 0.8818 (p) REVERT: C 72 ASN cc_start: 0.8375 (t0) cc_final: 0.7634 (t0) REVERT: C 88 ASP cc_start: 0.8552 (t0) cc_final: 0.8142 (t0) REVERT: C 103 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: C 107 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7777 (mtp180) REVERT: C 117 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8036 (tm-30) REVERT: D 25 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: D 66 MET cc_start: 0.8783 (mmm) cc_final: 0.8557 (mmm) REVERT: B 50 LYS cc_start: 0.8600 (ptmt) cc_final: 0.8255 (pptt) REVERT: B 59 LYS cc_start: 0.9233 (mmmm) cc_final: 0.8918 (mmmm) REVERT: B 63 ARG cc_start: 0.8860 (ttp-110) cc_final: 0.8641 (ttm110) REVERT: P 68 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: P 103 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8390 (mt0) REVERT: N 14 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8119 (tm-30) REVERT: N 64 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8252 (tmtm) REVERT: N 88 ASP cc_start: 0.8639 (t0) cc_final: 0.8169 (t0) REVERT: N 103 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8754 (mm-40) REVERT: N 117 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8164 (tm-30) REVERT: M 14 GLU cc_start: 0.8805 (tp30) cc_final: 0.8224 (mm-30) REVERT: M 17 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8743 (ttp80) REVERT: M 25 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8122 (mp10) REVERT: M 103 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: M 117 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7700 (tm-30) REVERT: O 37 ASN cc_start: 0.8502 (m110) cc_final: 0.8101 (OUTLIER) REVERT: O 59 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8840 (mmmm) REVERT: T 87 ASN cc_start: 0.9186 (m-40) cc_final: 0.8860 (m110) REVERT: R 14 GLU cc_start: 0.8843 (tp30) cc_final: 0.8174 (tm-30) REVERT: R 88 ASP cc_start: 0.8502 (t0) cc_final: 0.8139 (t0) REVERT: R 103 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8579 (mp10) REVERT: R 117 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8031 (tm-30) REVERT: Q 25 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: Q 100 ASN cc_start: 0.7984 (t0) cc_final: 0.7722 (t0) REVERT: Q 103 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: Q 134 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8390 (tm-30) REVERT: S 50 LYS cc_start: 0.8384 (pttm) cc_final: 0.8125 (pptt) REVERT: S 63 ARG cc_start: 0.8875 (ttp-110) cc_final: 0.8626 (ttm110) REVERT: X 484 GLU cc_start: 0.8865 (mp0) cc_final: 0.8582 (mp0) REVERT: E 68 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8695 (mm-40) REVERT: E 103 GLN cc_start: 0.8650 (mt0) cc_final: 0.8416 (mm110) REVERT: G 62 HIS cc_start: 0.8876 (t70) cc_final: 0.8558 (t-90) REVERT: G 63 ARG cc_start: 0.9239 (mtp85) cc_final: 0.8971 (ttp-110) REVERT: G 66 MET cc_start: 0.9440 (mmm) cc_final: 0.9229 (mmm) REVERT: G 72 ASN cc_start: 0.8762 (t0) cc_final: 0.8170 (t0) REVERT: G 87 ASN cc_start: 0.8715 (t0) cc_final: 0.8186 (t0) REVERT: G 88 ASP cc_start: 0.8506 (t0) cc_final: 0.8199 (t0) REVERT: G 101 ASN cc_start: 0.9112 (m-40) cc_final: 0.8682 (m110) REVERT: G 103 GLN cc_start: 0.9113 (mp10) cc_final: 0.8232 (mp10) REVERT: G 106 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7493 (mtp180) REVERT: G 117 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7850 (tm-30) REVERT: H 14 GLU cc_start: 0.8889 (tp30) cc_final: 0.8444 (tp30) REVERT: H 103 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7689 (mp10) REVERT: H 134 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7864 (mm110) REVERT: F 22 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8521 (tm) REVERT: F 50 LYS cc_start: 0.8703 (pptt) cc_final: 0.8024 (pptt) REVERT: F 59 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8862 (mmmm) REVERT: F 117 GLU cc_start: 0.8638 (pp20) cc_final: 0.8403 (pp20) outliers start: 115 outliers final: 65 residues processed: 698 average time/residue: 0.6243 time to fit residues: 487.9479 Evaluate side-chains 671 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 593 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 68 GLN Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 64 LYS Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 ASN Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain I residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 5.9990 chunk 53 optimal weight: 0.0470 chunk 105 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 205 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.7878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN C 58 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 134 GLN P 103 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 103 GLN T 134 GLN R 58 GLN R 68 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.102693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.074674 restraints weight = 39993.254| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.78 r_work: 0.2785 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20223 Z= 0.129 Angle : 0.614 9.559 27351 Z= 0.313 Chirality : 0.044 0.167 2905 Planarity : 0.003 0.038 3638 Dihedral : 4.302 35.276 2703 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.68 % Allowed : 28.93 % Favored : 66.39 % 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: 1.59 (0.18), residues: 2415 helix: 2.22 (0.20), residues: 644 sheet: 0.15 (0.19), residues: 714 loop : 1.20 (0.23), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 13 TYR 0.015 0.001 TYR N 20 PHE 0.016 0.002 PHE C 131 TRP 0.001 0.000 TRP K 509 HIS 0.007 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00293 (20223) covalent geometry : angle 0.61372 (27351) hydrogen bonds : bond 0.03338 ( 930) hydrogen bonds : angle 4.71368 ( 2691) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 665 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8810 (mmpt) REVERT: A 87 ASN cc_start: 0.9173 (m110) cc_final: 0.8675 (m110) REVERT: A 103 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8540 (mp10) REVERT: C 14 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 63 ARG cc_start: 0.9151 (ttm-80) cc_final: 0.8817 (ttp80) REVERT: C 71 THR cc_start: 0.9050 (m) cc_final: 0.8730 (p) REVERT: C 72 ASN cc_start: 0.8417 (t0) cc_final: 0.7643 (t0) REVERT: C 88 ASP cc_start: 0.8561 (t0) cc_final: 0.8071 (t0) REVERT: C 103 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8544 (mm-40) REVERT: C 107 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7852 (mtp180) REVERT: C 117 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 14 GLU cc_start: 0.8910 (tp30) cc_final: 0.8534 (tp30) REVERT: D 17 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8790 (ttp80) REVERT: D 25 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: D 66 MET cc_start: 0.8750 (mmm) cc_final: 0.8516 (mmm) REVERT: B 50 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8246 (pptt) REVERT: B 59 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8891 (mmmm) REVERT: B 63 ARG cc_start: 0.8851 (ttp-110) cc_final: 0.8594 (ttm110) REVERT: B 107 ARG cc_start: 0.8736 (mtt90) cc_final: 0.8524 (mtt90) REVERT: L 500 GLU cc_start: 0.8226 (tt0) cc_final: 0.7994 (tt0) REVERT: P 103 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8442 (mt0) REVERT: N 14 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7985 (tm-30) REVERT: N 88 ASP cc_start: 0.8565 (t0) cc_final: 0.8059 (t0) REVERT: N 103 GLN cc_start: 0.8921 (mm-40) cc_final: 0.8635 (mm-40) REVERT: N 117 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8061 (tm-30) REVERT: M 14 GLU cc_start: 0.8777 (tp30) cc_final: 0.8197 (mm-30) REVERT: M 25 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: M 59 LYS cc_start: 0.9129 (tttm) cc_final: 0.8863 (tttm) REVERT: M 95 MET cc_start: 0.8936 (mtt) cc_final: 0.8656 (mtp) REVERT: M 103 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: M 117 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7602 (tm-30) REVERT: O 37 ASN cc_start: 0.8451 (m110) cc_final: 0.8103 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8482 (pptt) cc_final: 0.8007 (pptt) REVERT: O 53 ASP cc_start: 0.9113 (m-30) cc_final: 0.8776 (m-30) REVERT: O 59 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8856 (mmmm) REVERT: O 60 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8670 (mm-30) REVERT: O 63 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8614 (ttm110) REVERT: O 107 ARG cc_start: 0.8838 (mtt90) cc_final: 0.8374 (mtt180) REVERT: T 87 ASN cc_start: 0.9172 (m-40) cc_final: 0.8831 (m110) REVERT: T 103 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8498 (mt0) REVERT: T 134 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8618 (tm130) REVERT: R 60 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: R 63 ARG cc_start: 0.9251 (mtp85) cc_final: 0.8971 (ttp-110) REVERT: R 88 ASP cc_start: 0.8472 (t0) cc_final: 0.8015 (t0) REVERT: R 99 SER cc_start: 0.8428 (m) cc_final: 0.8189 (p) REVERT: R 103 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8477 (mp10) REVERT: R 117 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8026 (tm-30) REVERT: Q 14 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8473 (tp30) REVERT: Q 59 LYS cc_start: 0.9106 (tttm) cc_final: 0.8843 (tttm) REVERT: Q 66 MET cc_start: 0.9032 (mmm) cc_final: 0.8794 (mmm) REVERT: Q 100 ASN cc_start: 0.7971 (t0) cc_final: 0.7660 (t0) REVERT: Q 103 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: Q 117 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7362 (pp20) REVERT: S 50 LYS cc_start: 0.8406 (pttm) cc_final: 0.8152 (pptt) REVERT: S 59 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8900 (mmmm) REVERT: S 60 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8645 (mm-30) REVERT: S 63 ARG cc_start: 0.8860 (ttp-110) cc_final: 0.8624 (ttm110) REVERT: X 484 GLU cc_start: 0.8864 (mp0) cc_final: 0.8566 (mp0) REVERT: E 68 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8669 (mm-40) REVERT: E 103 GLN cc_start: 0.8591 (mt0) cc_final: 0.8379 (mm110) REVERT: G 3 MET cc_start: 0.8412 (mmp) cc_final: 0.8167 (mmm) REVERT: G 62 HIS cc_start: 0.8849 (t70) cc_final: 0.8481 (t-90) REVERT: G 63 ARG cc_start: 0.9207 (mtp85) cc_final: 0.8952 (ttp-110) REVERT: G 66 MET cc_start: 0.9454 (mmm) cc_final: 0.9221 (mmm) REVERT: G 72 ASN cc_start: 0.8745 (t0) cc_final: 0.8140 (t0) REVERT: G 87 ASN cc_start: 0.8604 (t0) cc_final: 0.8044 (t0) REVERT: G 88 ASP cc_start: 0.8421 (t0) cc_final: 0.8070 (t0) REVERT: G 93 GLN cc_start: 0.9349 (tt0) cc_final: 0.9021 (tt0) REVERT: G 101 ASN cc_start: 0.9214 (m-40) cc_final: 0.8682 (m110) REVERT: G 103 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: G 107 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7593 (mtm-85) REVERT: H 14 GLU cc_start: 0.8801 (tp30) cc_final: 0.8407 (tp30) REVERT: H 103 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: H 134 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7864 (mm110) REVERT: F 59 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8876 (mmmm) REVERT: F 107 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8604 (mtt180) REVERT: F 123 LYS cc_start: 0.9077 (tttp) cc_final: 0.8844 (tttp) outliers start: 101 outliers final: 56 residues processed: 713 average time/residue: 0.6306 time to fit residues: 503.8730 Evaluate side-chains 686 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 617 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain T residue 134 GLN Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 502 ASP Chi-restraints excluded: chain W residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 3 optimal weight: 10.0000 chunk 169 optimal weight: 40.0000 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 214 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN C 58 GLN C 68 GLN D 134 GLN B 68 GLN B 128 ASN P 68 GLN P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 25 GLN O 68 GLN O 134 GLN T 68 GLN T 79 HIS T 103 GLN T 134 GLN R 58 GLN ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN S 134 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN H 69 ASN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.065752 restraints weight = 47680.809| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 4.12 r_work: 0.2584 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 20223 Z= 0.346 Angle : 0.711 10.683 27351 Z= 0.363 Chirality : 0.049 0.221 2905 Planarity : 0.004 0.040 3638 Dihedral : 4.862 43.094 2703 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 6.26 % Allowed : 27.96 % Favored : 65.79 % 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: 1.43 (0.18), residues: 2415 helix: 2.25 (0.20), residues: 620 sheet: -0.01 (0.18), residues: 718 loop : 1.08 (0.22), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 17 TYR 0.024 0.002 TYR O 20 PHE 0.023 0.002 PHE H 15 TRP 0.003 0.001 TRP K 509 HIS 0.005 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00806 (20223) covalent geometry : angle 0.71106 (27351) hydrogen bonds : bond 0.04155 ( 930) hydrogen bonds : angle 5.04567 ( 2691) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 622 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9233 (ttmt) cc_final: 0.8834 (mmtt) REVERT: A 87 ASN cc_start: 0.9087 (OUTLIER) cc_final: 0.8531 (m110) REVERT: A 117 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7621 (tp30) REVERT: C 14 GLU cc_start: 0.8599 (tm-30) cc_final: 0.7960 (tm-30) REVERT: C 63 ARG cc_start: 0.9194 (ttm-80) cc_final: 0.8859 (ttp80) REVERT: C 71 THR cc_start: 0.8874 (m) cc_final: 0.8495 (p) REVERT: C 72 ASN cc_start: 0.8248 (t0) cc_final: 0.7476 (t0) REVERT: C 88 ASP cc_start: 0.8689 (t0) cc_final: 0.8238 (t0) REVERT: C 103 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: C 107 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7663 (mtp180) REVERT: C 117 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8041 (tm-30) REVERT: D 14 GLU cc_start: 0.8907 (tp30) cc_final: 0.8661 (tp30) REVERT: D 25 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: D 66 MET cc_start: 0.8778 (mmm) cc_final: 0.8558 (mmm) REVERT: B 59 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8923 (mmmm) REVERT: B 63 ARG cc_start: 0.8834 (ttp-110) cc_final: 0.8606 (ttm110) REVERT: P 13 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8108 (mtm110) REVERT: P 103 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8249 (mt0) REVERT: N 14 GLU cc_start: 0.8609 (tm-30) cc_final: 0.7972 (tm-30) REVERT: N 88 ASP cc_start: 0.8679 (t0) cc_final: 0.8222 (t0) REVERT: N 103 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8694 (mm-40) REVERT: N 109 MET cc_start: 0.9095 (mtt) cc_final: 0.8634 (mtt) REVERT: N 117 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8159 (tm-30) REVERT: M 14 GLU cc_start: 0.8730 (tp30) cc_final: 0.8277 (mm-30) REVERT: M 17 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8661 (ttp80) REVERT: M 25 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: M 103 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: M 117 GLU cc_start: 0.8480 (tm-30) cc_final: 0.7670 (tm-30) REVERT: O 22 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8232 (tm) REVERT: O 37 ASN cc_start: 0.8564 (m110) cc_final: 0.8206 (OUTLIER) REVERT: O 59 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8869 (mmmm) REVERT: O 60 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8639 (mm-30) REVERT: O 63 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.8570 (ttm110) REVERT: T 87 ASN cc_start: 0.9099 (m-40) cc_final: 0.8663 (m110) REVERT: R 14 GLU cc_start: 0.8750 (tp30) cc_final: 0.8010 (tm-30) REVERT: R 63 ARG cc_start: 0.9264 (mtp85) cc_final: 0.8950 (ttp-110) REVERT: R 88 ASP cc_start: 0.8615 (t0) cc_final: 0.8203 (t0) REVERT: R 103 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8574 (mp10) REVERT: R 117 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8147 (tm-30) REVERT: Q 14 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8453 (tp30) REVERT: Q 17 ARG cc_start: 0.8905 (ttp80) cc_final: 0.8610 (ttp80) REVERT: Q 25 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8032 (mt0) REVERT: Q 100 ASN cc_start: 0.7791 (t0) cc_final: 0.7524 (t0) REVERT: Q 103 GLN cc_start: 0.8200 (mp10) cc_final: 0.7725 (mp10) REVERT: Q 134 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8390 (tm-30) REVERT: S 50 LYS cc_start: 0.8241 (pttm) cc_final: 0.8012 (pptt) REVERT: S 59 LYS cc_start: 0.9241 (mmmm) cc_final: 0.8975 (mmmm) REVERT: S 63 ARG cc_start: 0.8801 (ttp-110) cc_final: 0.8588 (ttm110) REVERT: X 484 GLU cc_start: 0.8856 (mp0) cc_final: 0.8502 (mp0) REVERT: E 68 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8650 (mm-40) REVERT: G 14 GLU cc_start: 0.8739 (tp30) cc_final: 0.8010 (tm-30) REVERT: G 62 HIS cc_start: 0.8823 (t70) cc_final: 0.8400 (t-90) REVERT: G 63 ARG cc_start: 0.9230 (mtp85) cc_final: 0.8971 (ttp80) REVERT: G 64 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8080 (tmtm) REVERT: G 66 MET cc_start: 0.9434 (mmm) cc_final: 0.9179 (mmm) REVERT: G 72 ASN cc_start: 0.8619 (t0) cc_final: 0.8038 (t0) REVERT: G 87 ASN cc_start: 0.8801 (t0) cc_final: 0.8264 (t0) REVERT: G 88 ASP cc_start: 0.8629 (t0) cc_final: 0.8309 (t0) REVERT: G 101 ASN cc_start: 0.9203 (m-40) cc_final: 0.8690 (m-40) REVERT: G 103 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: G 107 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7606 (mtm-85) REVERT: G 117 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8006 (tm-30) REVERT: H 25 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8196 (mt0) REVERT: H 103 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7536 (mp10) REVERT: F 22 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8305 (tm) REVERT: F 50 LYS cc_start: 0.8614 (pptt) cc_final: 0.8385 (pmtt) REVERT: F 59 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8934 (mmmm) outliers start: 135 outliers final: 77 residues processed: 702 average time/residue: 0.6846 time to fit residues: 536.3298 Evaluate side-chains 688 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 596 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 107 ARG Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 13 ARG Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 88 ASP Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain V residue 490 LEU Chi-restraints excluded: chain V residue 497 LEU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 101 ASN Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 497 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 106 ARG Chi-restraints excluded: chain G residue 107 ARG Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 25 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 492 THR Chi-restraints excluded: chain I residue 497 LEU Chi-restraints excluded: chain I residue 505 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 98 optimal weight: 0.1980 chunk 151 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 68 GLN D 134 GLN B 24 ASN P 68 GLN P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 HIS ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 79 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.074234 restraints weight = 41221.465| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.84 r_work: 0.2764 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20223 Z= 0.135 Angle : 0.662 11.052 27351 Z= 0.333 Chirality : 0.045 0.177 2905 Planarity : 0.004 0.049 3638 Dihedral : 4.382 35.767 2703 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.68 % Allowed : 29.81 % Favored : 65.51 % 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: 1.58 (0.18), residues: 2415 helix: 2.36 (0.20), residues: 624 sheet: 0.17 (0.19), residues: 698 loop : 1.08 (0.22), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 63 TYR 0.016 0.001 TYR C 20 PHE 0.015 0.002 PHE N 131 TRP 0.001 0.000 TRP I 509 HIS 0.006 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00310 (20223) covalent geometry : angle 0.66218 (27351) hydrogen bonds : bond 0.03410 ( 930) hydrogen bonds : angle 4.76569 ( 2691) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 648 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8868 (mmtm) REVERT: A 87 ASN cc_start: 0.9193 (OUTLIER) cc_final: 0.8735 (m110) REVERT: C 14 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 63 ARG cc_start: 0.9166 (ttm-80) cc_final: 0.8854 (ttp80) REVERT: C 71 THR cc_start: 0.8930 (m) cc_final: 0.8544 (p) REVERT: C 72 ASN cc_start: 0.8298 (t0) cc_final: 0.7556 (t0) REVERT: C 88 ASP cc_start: 0.8680 (t0) cc_final: 0.8160 (t0) REVERT: C 103 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: C 117 GLU cc_start: 0.8566 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 25 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: D 66 MET cc_start: 0.8726 (mmm) cc_final: 0.8481 (mmm) REVERT: B 50 LYS cc_start: 0.8552 (ptmt) cc_final: 0.8274 (pptt) REVERT: B 59 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8899 (mmmm) REVERT: B 60 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8614 (mm-30) REVERT: B 63 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8603 (ttm110) REVERT: P 103 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: P 134 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8707 (tm130) REVERT: N 3 MET cc_start: 0.8410 (mmp) cc_final: 0.8126 (tpp) REVERT: N 14 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8010 (tm-30) REVERT: N 88 ASP cc_start: 0.8584 (t0) cc_final: 0.8081 (t0) REVERT: N 103 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8538 (mm-40) REVERT: N 109 MET cc_start: 0.8988 (mtt) cc_final: 0.8496 (mtt) REVERT: N 117 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8087 (tm-30) REVERT: M 14 GLU cc_start: 0.8744 (tp30) cc_final: 0.8193 (mm-30) REVERT: M 25 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8103 (mp10) REVERT: M 95 MET cc_start: 0.8984 (mtt) cc_final: 0.8476 (mtp) REVERT: M 103 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7406 (mp10) REVERT: M 117 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7554 (tm-30) REVERT: O 37 ASN cc_start: 0.8460 (m110) cc_final: 0.8144 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8551 (pptt) cc_final: 0.8087 (pptt) REVERT: O 53 ASP cc_start: 0.9132 (m-30) cc_final: 0.8736 (m-30) REVERT: O 59 LYS cc_start: 0.9218 (mmmm) cc_final: 0.8855 (mmmm) REVERT: O 60 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8617 (mm-30) REVERT: O 63 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8562 (ttm110) REVERT: T 87 ASN cc_start: 0.9178 (m-40) cc_final: 0.8575 (m110) REVERT: T 103 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8463 (mt0) REVERT: T 134 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8801 (tm130) REVERT: R 63 ARG cc_start: 0.9279 (mtp85) cc_final: 0.8999 (ttp-110) REVERT: R 88 ASP cc_start: 0.8546 (t0) cc_final: 0.8114 (t0) REVERT: R 103 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8423 (mp10) REVERT: R 117 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8086 (tm-30) REVERT: Q 14 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8346 (mm-30) REVERT: Q 17 ARG cc_start: 0.8926 (ttp80) cc_final: 0.8699 (ttp80) REVERT: Q 25 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: Q 100 ASN cc_start: 0.7945 (t0) cc_final: 0.7608 (t0) REVERT: Q 103 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: S 50 LYS cc_start: 0.8350 (pttm) cc_final: 0.8102 (pptt) REVERT: S 59 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8909 (mmmm) REVERT: S 60 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8661 (mm-30) REVERT: S 63 ARG cc_start: 0.8842 (ttp-110) cc_final: 0.8587 (ttm110) REVERT: S 87 ASN cc_start: 0.9268 (m-40) cc_final: 0.8869 (m-40) REVERT: X 484 GLU cc_start: 0.8872 (mp0) cc_final: 0.8573 (mp0) REVERT: E 68 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8605 (mm-40) REVERT: E 103 GLN cc_start: 0.8576 (mt0) cc_final: 0.8348 (mm110) REVERT: G 62 HIS cc_start: 0.8874 (t70) cc_final: 0.8458 (t-90) REVERT: G 63 ARG cc_start: 0.9224 (mtp85) cc_final: 0.8963 (ttp-110) REVERT: G 66 MET cc_start: 0.9461 (mmm) cc_final: 0.9258 (mmm) REVERT: G 72 ASN cc_start: 0.8641 (t0) cc_final: 0.8036 (t0) REVERT: G 87 ASN cc_start: 0.8623 (t0) cc_final: 0.8041 (t0) REVERT: G 88 ASP cc_start: 0.8539 (t0) cc_final: 0.8127 (t0) REVERT: G 93 GLN cc_start: 0.9377 (tt0) cc_final: 0.9046 (tt0) REVERT: G 101 ASN cc_start: 0.9296 (m-40) cc_final: 0.8678 (m110) REVERT: G 103 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8330 (mp10) REVERT: H 103 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: H 117 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7304 (pp20) REVERT: F 50 LYS cc_start: 0.8679 (pptt) cc_final: 0.8439 (pmtt) REVERT: F 59 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8901 (mmmm) outliers start: 101 outliers final: 57 residues processed: 699 average time/residue: 0.6726 time to fit residues: 525.7638 Evaluate side-chains 684 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 616 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 134 GLN Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 134 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 497 LEU Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain I residue 492 THR Chi-restraints excluded: chain I residue 497 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 208 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 68 GLN D 122 ASN B 68 GLN P 68 GLN P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 79 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN R 68 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 GLN S 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.066984 restraints weight = 62539.547| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 4.55 r_work: 0.2648 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 20223 Z= 0.255 Angle : 0.709 11.299 27351 Z= 0.356 Chirality : 0.047 0.229 2905 Planarity : 0.004 0.059 3638 Dihedral : 4.593 36.052 2702 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.05 % Allowed : 30.27 % Favored : 64.67 % 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: 1.49 (0.18), residues: 2415 helix: 2.27 (0.20), residues: 624 sheet: 0.10 (0.19), residues: 698 loop : 1.06 (0.22), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 13 TYR 0.020 0.002 TYR O 20 PHE 0.020 0.002 PHE H 15 TRP 0.002 0.000 TRP K 509 HIS 0.005 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00597 (20223) covalent geometry : angle 0.70866 (27351) hydrogen bonds : bond 0.03875 ( 930) hydrogen bonds : angle 4.89688 ( 2691) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 605 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8836 (mmpt) REVERT: A 87 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8702 (m110) REVERT: C 14 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 63 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8874 (ttp80) REVERT: C 71 THR cc_start: 0.8870 (m) cc_final: 0.8483 (p) REVERT: C 72 ASN cc_start: 0.8239 (t0) cc_final: 0.7696 (t0) REVERT: C 88 ASP cc_start: 0.8772 (t0) cc_final: 0.8306 (t0) REVERT: C 103 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: C 107 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7987 (mtm180) REVERT: C 117 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 25 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: D 66 MET cc_start: 0.8817 (mmm) cc_final: 0.8592 (mmm) REVERT: B 50 LYS cc_start: 0.8517 (ptmt) cc_final: 0.8252 (pptt) REVERT: B 59 LYS cc_start: 0.9254 (mmmm) cc_final: 0.8934 (mmmm) REVERT: B 63 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8630 (ttm110) REVERT: B 107 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8553 (mtt90) REVERT: P 13 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8195 (mtm110) REVERT: P 103 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: N 14 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8031 (tm-30) REVERT: N 88 ASP cc_start: 0.8676 (t0) cc_final: 0.8212 (t0) REVERT: N 103 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8564 (mp10) REVERT: N 117 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8189 (tm-30) REVERT: M 14 GLU cc_start: 0.8796 (tp30) cc_final: 0.8499 (tp30) REVERT: M 17 ARG cc_start: 0.8988 (ttp80) cc_final: 0.8748 (ttp80) REVERT: M 25 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8076 (mp10) REVERT: M 103 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7637 (mp10) REVERT: M 117 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7751 (tm-30) REVERT: O 37 ASN cc_start: 0.8576 (m110) cc_final: 0.8262 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8496 (pptt) cc_final: 0.8072 (pptt) REVERT: O 59 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8888 (mmmm) REVERT: V 484 GLU cc_start: 0.8829 (mp0) cc_final: 0.8612 (mp0) REVERT: T 87 ASN cc_start: 0.9152 (m-40) cc_final: 0.8783 (m110) REVERT: T 103 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8648 (mp10) REVERT: T 134 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8903 (tm-30) REVERT: R 14 GLU cc_start: 0.8850 (tp30) cc_final: 0.8201 (tm-30) REVERT: R 63 ARG cc_start: 0.9278 (mtp85) cc_final: 0.8974 (ttp80) REVERT: R 88 ASP cc_start: 0.8672 (t0) cc_final: 0.8282 (t0) REVERT: R 103 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8609 (mp10) REVERT: R 117 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8162 (tm-30) REVERT: Q 14 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8512 (mm-30) REVERT: Q 25 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: Q 100 ASN cc_start: 0.7948 (t0) cc_final: 0.7737 (t0) REVERT: Q 103 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: Q 117 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7521 (pp20) REVERT: S 50 LYS cc_start: 0.8311 (pttm) cc_final: 0.8081 (pptt) REVERT: S 59 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8938 (mmmm) REVERT: S 60 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8673 (mm-30) REVERT: S 63 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8609 (ttm110) REVERT: S 107 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8594 (mtp85) REVERT: X 484 GLU cc_start: 0.8860 (mp0) cc_final: 0.8475 (mp0) REVERT: X 504 LEU cc_start: 0.8719 (mp) cc_final: 0.8460 (mp) REVERT: E 68 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8723 (mm-40) REVERT: E 103 GLN cc_start: 0.8681 (mt0) cc_final: 0.8426 (mm110) REVERT: G 14 GLU cc_start: 0.8819 (tp30) cc_final: 0.8170 (tm-30) REVERT: G 62 HIS cc_start: 0.8894 (t70) cc_final: 0.8437 (t-90) REVERT: G 63 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8987 (ttp80) REVERT: G 66 MET cc_start: 0.9471 (mmm) cc_final: 0.9237 (mmm) REVERT: G 72 ASN cc_start: 0.8640 (t0) cc_final: 0.8030 (t0) REVERT: G 87 ASN cc_start: 0.8777 (t0) cc_final: 0.8224 (t0) REVERT: G 88 ASP cc_start: 0.8673 (t0) cc_final: 0.8312 (t0) REVERT: G 101 ASN cc_start: 0.9283 (m-40) cc_final: 0.8675 (m-40) REVERT: G 103 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: H 17 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8782 (ttp80) REVERT: H 103 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7718 (mp10) REVERT: H 117 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: F 50 LYS cc_start: 0.8681 (pptt) cc_final: 0.8415 (pmtt) REVERT: F 59 LYS cc_start: 0.9268 (mmmm) cc_final: 0.8954 (mmmm) REVERT: F 123 LYS cc_start: 0.9030 (tttp) cc_final: 0.8801 (tppt) outliers start: 109 outliers final: 71 residues processed: 675 average time/residue: 0.6960 time to fit residues: 524.0232 Evaluate side-chains 673 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 589 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 13 ARG Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 474 THR Chi-restraints excluded: chain V residue 497 LEU Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 107 ARG Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain X residue 474 THR Chi-restraints excluded: chain X residue 497 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 497 LEU Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 492 THR Chi-restraints excluded: chain I residue 505 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 68 GLN B 68 GLN P 68 GLN P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 79 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN R 68 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 134 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.101178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072579 restraints weight = 46749.830| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.05 r_work: 0.2731 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20223 Z= 0.155 Angle : 0.697 11.802 27351 Z= 0.348 Chirality : 0.046 0.194 2905 Planarity : 0.004 0.059 3638 Dihedral : 4.416 35.144 2702 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.22 % Allowed : 31.39 % Favored : 64.39 % 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: 1.54 (0.18), residues: 2415 helix: 2.31 (0.20), residues: 624 sheet: 0.14 (0.19), residues: 698 loop : 1.07 (0.22), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 13 TYR 0.017 0.001 TYR C 20 PHE 0.016 0.002 PHE R 131 TRP 0.001 0.000 TRP I 509 HIS 0.006 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00360 (20223) covalent geometry : angle 0.69705 (27351) hydrogen bonds : bond 0.03541 ( 930) hydrogen bonds : angle 4.79612 ( 2691) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 616 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9197 (ttmt) cc_final: 0.8843 (mmtt) REVERT: A 87 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8692 (m110) REVERT: A 103 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8554 (mp10) REVERT: C 14 GLU cc_start: 0.8674 (tm-30) cc_final: 0.7986 (tm-30) REVERT: C 63 ARG cc_start: 0.9151 (ttm-80) cc_final: 0.8852 (ttp80) REVERT: C 71 THR cc_start: 0.8903 (m) cc_final: 0.8353 (p) REVERT: C 72 ASN cc_start: 0.8194 (t0) cc_final: 0.7915 (t0) REVERT: C 88 ASP cc_start: 0.8706 (t0) cc_final: 0.8189 (t0) REVERT: C 101 ASN cc_start: 0.9271 (m-40) cc_final: 0.8452 (m110) REVERT: C 103 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: C 107 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7877 (mtm180) REVERT: C 117 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 17 ARG cc_start: 0.9001 (ttp80) cc_final: 0.8796 (ttp80) REVERT: D 25 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8025 (mt0) REVERT: D 66 MET cc_start: 0.8730 (mmm) cc_final: 0.8518 (mmm) REVERT: B 50 LYS cc_start: 0.8536 (ptmt) cc_final: 0.8260 (pptt) REVERT: B 59 LYS cc_start: 0.9238 (mmmm) cc_final: 0.8885 (mmmm) REVERT: B 63 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8635 (ttm110) REVERT: L 500 GLU cc_start: 0.8226 (tt0) cc_final: 0.7994 (tt0) REVERT: P 103 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8297 (mt0) REVERT: P 134 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8572 (tm130) REVERT: N 14 GLU cc_start: 0.8653 (tm-30) cc_final: 0.7982 (tm-30) REVERT: N 88 ASP cc_start: 0.8616 (t0) cc_final: 0.8121 (t0) REVERT: N 103 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8776 (mm-40) REVERT: N 109 MET cc_start: 0.8861 (mtt) cc_final: 0.8346 (mtt) REVERT: N 117 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8146 (tm-30) REVERT: M 14 GLU cc_start: 0.8750 (tp30) cc_final: 0.8527 (tp30) REVERT: M 17 ARG cc_start: 0.8985 (ttp80) cc_final: 0.8719 (ttp80) REVERT: M 25 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8097 (mp10) REVERT: M 103 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: M 117 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7557 (tm-30) REVERT: O 37 ASN cc_start: 0.8491 (m110) cc_final: 0.8190 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8573 (pptt) cc_final: 0.8111 (pptt) REVERT: O 53 ASP cc_start: 0.9133 (m-30) cc_final: 0.8751 (m-30) REVERT: O 59 LYS cc_start: 0.9236 (mmmm) cc_final: 0.8885 (mmmm) REVERT: O 63 ARG cc_start: 0.8852 (ttp-110) cc_final: 0.8614 (ttp-110) REVERT: O 107 ARG cc_start: 0.8812 (mtt90) cc_final: 0.8379 (mtt180) REVERT: V 484 GLU cc_start: 0.8844 (mp0) cc_final: 0.8643 (mp0) REVERT: T 87 ASN cc_start: 0.9178 (m-40) cc_final: 0.8540 (m110) REVERT: T 103 GLN cc_start: 0.8825 (mm-40) cc_final: 0.8490 (mt0) REVERT: T 134 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8600 (tm130) REVERT: R 14 GLU cc_start: 0.8798 (tp30) cc_final: 0.8131 (tm-30) REVERT: R 63 ARG cc_start: 0.9275 (mtp85) cc_final: 0.8955 (ttp80) REVERT: R 68 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8039 (mt0) REVERT: R 88 ASP cc_start: 0.8588 (t0) cc_final: 0.8181 (t0) REVERT: R 103 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8640 (mp10) REVERT: R 117 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8104 (tm-30) REVERT: Q 14 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8374 (mm-30) REVERT: Q 17 ARG cc_start: 0.8964 (ttp80) cc_final: 0.8712 (ttp80) REVERT: Q 25 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: Q 100 ASN cc_start: 0.7955 (t0) cc_final: 0.7663 (t0) REVERT: Q 103 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: Q 117 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: S 50 LYS cc_start: 0.8323 (pttm) cc_final: 0.8089 (pptt) REVERT: S 59 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8884 (mmmm) REVERT: S 60 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8661 (mm-30) REVERT: S 63 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8584 (ttm110) REVERT: S 87 ASN cc_start: 0.9264 (m-40) cc_final: 0.8782 (m-40) REVERT: S 107 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8601 (mtp85) REVERT: X 484 GLU cc_start: 0.8847 (mp0) cc_final: 0.8526 (mp0) REVERT: X 500 GLU cc_start: 0.8362 (tt0) cc_final: 0.8132 (tt0) REVERT: X 504 LEU cc_start: 0.8603 (mp) cc_final: 0.8371 (mp) REVERT: E 68 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8638 (mm-40) REVERT: E 103 GLN cc_start: 0.8610 (mt0) cc_final: 0.8368 (mm110) REVERT: G 62 HIS cc_start: 0.8872 (t70) cc_final: 0.8401 (t-90) REVERT: G 63 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8995 (ttp80) REVERT: G 66 MET cc_start: 0.9461 (mmm) cc_final: 0.9239 (mmm) REVERT: G 72 ASN cc_start: 0.8615 (t0) cc_final: 0.7997 (t0) REVERT: G 87 ASN cc_start: 0.8672 (t0) cc_final: 0.8104 (t0) REVERT: G 88 ASP cc_start: 0.8615 (t0) cc_final: 0.8177 (t0) REVERT: G 101 ASN cc_start: 0.9287 (m-40) cc_final: 0.8641 (m110) REVERT: G 103 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8425 (mp10) REVERT: H 14 GLU cc_start: 0.8913 (tp30) cc_final: 0.8678 (tp30) REVERT: H 17 ARG cc_start: 0.9036 (ttp80) cc_final: 0.8704 (ttp80) REVERT: H 103 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: H 117 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: H 123 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8548 (ttmt) REVERT: F 50 LYS cc_start: 0.8680 (pptt) cc_final: 0.8395 (pmtt) REVERT: F 59 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8907 (mmmm) REVERT: F 107 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8427 (mtt180) REVERT: F 123 LYS cc_start: 0.9003 (tttp) cc_final: 0.8788 (tppt) REVERT: W 492 THR cc_start: 0.8465 (p) cc_final: 0.8103 (p) outliers start: 91 outliers final: 61 residues processed: 666 average time/residue: 0.6610 time to fit residues: 491.6317 Evaluate side-chains 687 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 612 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 134 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 68 GLN Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 107 ARG Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain X residue 497 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 492 THR Chi-restraints excluded: chain I residue 497 LEU Chi-restraints excluded: chain I residue 505 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 227 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 224 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 54 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 69 ASN A 134 GLN C 58 GLN C 68 GLN B 68 GLN ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 79 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN R 68 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN H 68 GLN ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.069796 restraints weight = 59414.562| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.55 r_work: 0.2697 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20223 Z= 0.174 Angle : 0.712 12.317 27351 Z= 0.355 Chirality : 0.046 0.200 2905 Planarity : 0.004 0.047 3638 Dihedral : 4.428 34.448 2702 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.13 % Allowed : 31.76 % Favored : 64.12 % 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: 1.55 (0.18), residues: 2415 helix: 2.31 (0.20), residues: 624 sheet: 0.15 (0.18), residues: 698 loop : 1.07 (0.22), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 63 TYR 0.017 0.001 TYR C 20 PHE 0.016 0.002 PHE B 131 TRP 0.001 0.000 TRP K 509 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00407 (20223) covalent geometry : angle 0.71246 (27351) hydrogen bonds : bond 0.03587 ( 930) hydrogen bonds : angle 4.78981 ( 2691) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 615 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9233 (ttmt) cc_final: 0.8846 (mmpt) REVERT: A 87 ASN cc_start: 0.9183 (OUTLIER) cc_final: 0.8732 (m110) REVERT: A 103 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8586 (mp10) REVERT: C 14 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 63 ARG cc_start: 0.9170 (ttm-80) cc_final: 0.8862 (ttp80) REVERT: C 71 THR cc_start: 0.8894 (m) cc_final: 0.8346 (p) REVERT: C 72 ASN cc_start: 0.8183 (t0) cc_final: 0.7858 (t0) REVERT: C 88 ASP cc_start: 0.8738 (t0) cc_final: 0.8243 (t0) REVERT: C 101 ASN cc_start: 0.9261 (m-40) cc_final: 0.8452 (m110) REVERT: C 103 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8225 (mp10) REVERT: C 117 GLU cc_start: 0.8584 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 17 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8716 (ttp80) REVERT: D 25 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: D 66 MET cc_start: 0.8782 (mmm) cc_final: 0.8574 (mmm) REVERT: B 50 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8289 (pptt) REVERT: B 59 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8888 (mmmm) REVERT: B 63 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8639 (ttm110) REVERT: P 103 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: P 134 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8680 (tm-30) REVERT: N 3 MET cc_start: 0.8390 (mmp) cc_final: 0.8083 (tpp) REVERT: N 14 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8031 (tm-30) REVERT: N 88 ASP cc_start: 0.8641 (t0) cc_final: 0.8147 (t0) REVERT: N 103 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8771 (mm-40) REVERT: N 117 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8157 (tm-30) REVERT: M 14 GLU cc_start: 0.8800 (tp30) cc_final: 0.8398 (tp30) REVERT: M 17 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8756 (ttp80) REVERT: M 25 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: M 95 MET cc_start: 0.8995 (mtt) cc_final: 0.8721 (mtp) REVERT: M 103 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: M 117 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7591 (tm-30) REVERT: O 37 ASN cc_start: 0.8516 (m110) cc_final: 0.8209 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8570 (pptt) cc_final: 0.8132 (pptt) REVERT: O 59 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8891 (mmmm) REVERT: O 60 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8691 (mm-30) REVERT: O 63 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8652 (ttp-110) REVERT: O 107 ARG cc_start: 0.8878 (mtt90) cc_final: 0.8426 (mtt180) REVERT: V 484 GLU cc_start: 0.8851 (mp0) cc_final: 0.8647 (mp0) REVERT: T 87 ASN cc_start: 0.9183 (m-40) cc_final: 0.8571 (m110) REVERT: T 95 MET cc_start: 0.9282 (mtp) cc_final: 0.9016 (mtp) REVERT: T 103 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8629 (mp10) REVERT: T 134 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8689 (tm130) REVERT: R 14 GLU cc_start: 0.8836 (tp30) cc_final: 0.8175 (tm-30) REVERT: R 63 ARG cc_start: 0.9301 (mtp85) cc_final: 0.8991 (ttp80) REVERT: R 88 ASP cc_start: 0.8644 (t0) cc_final: 0.8222 (t0) REVERT: R 103 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8662 (mp10) REVERT: R 107 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7364 (ttm170) REVERT: R 117 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8118 (tm-30) REVERT: Q 14 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8410 (mm-30) REVERT: Q 17 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8728 (ttp80) REVERT: Q 25 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: Q 100 ASN cc_start: 0.8023 (t0) cc_final: 0.7750 (t0) REVERT: Q 103 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: Q 117 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: Q 134 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8019 (tm-30) REVERT: S 50 LYS cc_start: 0.8312 (pttm) cc_final: 0.8074 (pptt) REVERT: S 59 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8890 (mmmm) REVERT: S 60 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8659 (mm-30) REVERT: S 63 ARG cc_start: 0.8869 (ttp-110) cc_final: 0.8605 (ttm110) REVERT: S 87 ASN cc_start: 0.9251 (m-40) cc_final: 0.8754 (m-40) REVERT: S 107 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8658 (mtp85) REVERT: X 484 GLU cc_start: 0.8864 (mp0) cc_final: 0.8540 (mp0) REVERT: X 504 LEU cc_start: 0.8632 (mp) cc_final: 0.8408 (mp) REVERT: E 68 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8652 (mm-40) REVERT: E 103 GLN cc_start: 0.8654 (mt0) cc_final: 0.8412 (mm110) REVERT: G 14 GLU cc_start: 0.8808 (tp30) cc_final: 0.8120 (tm-30) REVERT: G 62 HIS cc_start: 0.8897 (t70) cc_final: 0.8428 (t-90) REVERT: G 63 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8993 (ttp80) REVERT: G 66 MET cc_start: 0.9479 (mmm) cc_final: 0.9254 (mmm) REVERT: G 72 ASN cc_start: 0.8623 (t0) cc_final: 0.8005 (t0) REVERT: G 87 ASN cc_start: 0.8714 (t0) cc_final: 0.8147 (t0) REVERT: G 88 ASP cc_start: 0.8659 (t0) cc_final: 0.8221 (t0) REVERT: G 101 ASN cc_start: 0.9274 (m-40) cc_final: 0.8630 (m110) REVERT: G 103 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8427 (mp10) REVERT: H 17 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8766 (ttp80) REVERT: H 103 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: H 117 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: H 123 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8564 (ttmt) REVERT: F 50 LYS cc_start: 0.8661 (pptt) cc_final: 0.8366 (pmtt) REVERT: F 59 LYS cc_start: 0.9273 (mmmm) cc_final: 0.8962 (mmmm) REVERT: F 107 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8468 (mtt180) REVERT: F 123 LYS cc_start: 0.9007 (tttp) cc_final: 0.8785 (tppt) REVERT: W 492 THR cc_start: 0.8497 (p) cc_final: 0.8134 (p) outliers start: 89 outliers final: 65 residues processed: 666 average time/residue: 0.6296 time to fit residues: 467.7199 Evaluate side-chains 682 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 604 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 25 GLN Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 103 GLN Chi-restraints excluded: chain P residue 134 GLN Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 73 CYS Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 41 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 107 ARG Chi-restraints excluded: chain S residue 120 VAL Chi-restraints excluded: chain X residue 497 LEU Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 36 LYS Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 GLN Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain K residue 485 SER Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 485 SER Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 492 THR Chi-restraints excluded: chain I residue 505 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 135 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 134 GLN C 58 GLN C 68 GLN B 68 GLN ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN P 134 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 79 HIS ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN R 68 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** E 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN F 68 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.071063 restraints weight = 51134.524| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 4.29 r_work: 0.2723 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20223 Z= 0.155 Angle : 0.717 12.192 27351 Z= 0.356 Chirality : 0.046 0.182 2905 Planarity : 0.004 0.047 3638 Dihedral : 4.396 33.529 2702 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.59 % Allowed : 31.25 % Favored : 64.16 % 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: 1.55 (0.18), residues: 2415 helix: 2.12 (0.20), residues: 644 sheet: 0.23 (0.18), residues: 690 loop : 1.11 (0.22), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 63 TYR 0.017 0.001 TYR C 20 PHE 0.015 0.002 PHE B 131 TRP 0.001 0.000 TRP I 509 HIS 0.006 0.000 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00362 (20223) covalent geometry : angle 0.71708 (27351) hydrogen bonds : bond 0.03524 ( 930) hydrogen bonds : angle 4.77884 ( 2691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9887.35 seconds wall clock time: 168 minutes 45.74 seconds (10125.74 seconds total)