Starting phenix.real_space_refine on Tue Jun 17 04:15:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivq_60932/06_2025/9ivq_60932.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivq_60932/06_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_60932/06_2025/9ivq_60932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivq_60932/06_2025/9ivq_60932.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivq_60932/06_2025/9ivq_60932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivq_60932/06_2025/9ivq_60932.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.88, per 1000 atoms: 0.65 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: 4.76 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.69 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: 6.83 Time building geometry restraints manager: 5.70 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: 2.520 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 47.450 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.190 ------------------------------------------------------------------------------- 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 : 10.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (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 TRP 0.001 0.000 TRP U 509 HIS 0.007 0.001 HIS E 79 PHE 0.015 0.002 PHE O 15 TYR 0.015 0.001 TYR H 133 ARG 0.012 0.001 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.10761 ( 930) hydrogen bonds : angle 5.70339 ( 2691) covalent geometry : bond 0.00555 (20223) covalent geometry : angle 0.88565 (27351) *********************** 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 : 2.104 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: 0.8539 (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: 0.8271 (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: 0.8327 (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: 1.3678 time to fit residues: 1086.4864 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 : 2.133 ------------------------------------------------------------------------------- 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 195 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 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 24 ASN 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 ** S 24 ASN ** 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 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 = 0.3372 r_free = 0.3372 target = 0.100882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070954 restraints weight = 56249.105| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.49 r_work: 0.2724 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20223 Z= 0.164 Angle : 0.600 7.455 27351 Z= 0.314 Chirality : 0.045 0.166 2905 Planarity : 0.004 0.045 3638 Dihedral : 4.875 52.888 2733 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.91 % Allowed : 25.96 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.19), residues: 2415 helix: 2.34 (0.21), residues: 620 sheet: -0.09 (0.18), residues: 772 loop : 1.37 (0.24), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP K 509 HIS 0.008 0.001 HIS E 79 PHE 0.015 0.002 PHE B 15 TYR 0.015 0.001 TYR F 40 ARG 0.009 0.001 ARG M 17 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 930) hydrogen bonds : angle 4.91707 ( 2691) covalent geometry : bond 0.00376 (20223) covalent geometry : angle 0.60049 (27351) *********************** 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: 106 poor density : 647 time to evaluate : 2.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9229 (ttmt) cc_final: 0.8920 (mmtm) REVERT: A 87 ASN cc_start: 0.9201 (m110) cc_final: 0.8822 (m110) REVERT: C 14 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 63 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8831 (ttp80) REVERT: C 72 ASN cc_start: 0.8418 (t0) cc_final: 0.7783 (t0) REVERT: C 88 ASP cc_start: 0.8399 (t0) cc_final: 0.8084 (t0) REVERT: C 103 GLN cc_start: 0.9039 (mp10) cc_final: 0.8622 (mp10) REVERT: C 117 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 14 GLU cc_start: 0.8979 (tp30) cc_final: 0.8649 (tp30) REVERT: D 117 GLU cc_start: 0.8709 (tp30) cc_final: 0.8082 (tm-30) REVERT: B 50 LYS cc_start: 0.8662 (ptmt) cc_final: 0.8280 (pptt) REVERT: B 63 ARG cc_start: 0.8805 (ttp-110) cc_final: 0.8541 (ttm110) REVERT: P 87 ASN cc_start: 0.8994 (m-40) cc_final: 0.8777 (m-40) REVERT: N 3 MET cc_start: 0.8521 (mmm) cc_final: 0.8291 (tpp) REVERT: N 14 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8179 (tm-30) REVERT: N 62 HIS cc_start: 0.8840 (t-90) cc_final: 0.8604 (t70) REVERT: N 64 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8228 (tmtm) REVERT: N 88 ASP cc_start: 0.8543 (t0) cc_final: 0.8029 (t0) REVERT: N 103 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8638 (mm-40) REVERT: N 117 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8172 (tm-30) REVERT: M 14 GLU cc_start: 0.8816 (tp30) cc_final: 0.8313 (mm-30) REVERT: M 17 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8749 (ttp80) REVERT: M 25 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8195 (mp10) REVERT: M 103 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: M 123 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8422 (tttp) REVERT: O 59 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8822 (mmmm) REVERT: T 87 ASN cc_start: 0.9283 (m-40) cc_final: 0.8944 (m-40) REVERT: T 103 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8513 (mm110) REVERT: R 63 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8942 (ttp80) REVERT: R 72 ASN cc_start: 0.8209 (t0) cc_final: 0.7658 (t0) REVERT: R 88 ASP cc_start: 0.8376 (t0) cc_final: 0.8124 (t0) REVERT: R 99 SER cc_start: 0.8307 (m) cc_final: 0.7896 (p) REVERT: R 102 ASN cc_start: 0.9033 (m110) cc_final: 0.8704 (m110) REVERT: R 103 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8735 (mm-40) REVERT: R 117 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8176 (tm-30) REVERT: Q 14 GLU cc_start: 0.8846 (tp30) cc_final: 0.8561 (mm-30) REVERT: Q 66 MET cc_start: 0.9091 (mmm) cc_final: 0.8864 (mmm) REVERT: Q 71 THR cc_start: 0.9142 (t) cc_final: 0.8661 (p) REVERT: Q 103 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: S 50 LYS cc_start: 0.8490 (pttm) cc_final: 0.8203 (pptt) REVERT: S 87 ASN cc_start: 0.9247 (m-40) cc_final: 0.8984 (m110) REVERT: X 484 GLU cc_start: 0.8918 (mp0) cc_final: 0.8609 (mp0) REVERT: X 500 GLU cc_start: 0.8369 (tt0) cc_final: 0.8116 (tt0) REVERT: E 68 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8703 (mm-40) REVERT: E 103 GLN cc_start: 0.8607 (mt0) cc_final: 0.8403 (mm110) REVERT: E 117 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8376 (mm-30) REVERT: G 25 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8740 (mm110) REVERT: G 66 MET cc_start: 0.9449 (mmm) cc_final: 0.9213 (mmm) REVERT: G 69 ASN cc_start: 0.8719 (p0) cc_final: 0.8446 (p0) REVERT: G 87 ASN cc_start: 0.8611 (t0) cc_final: 0.8099 (t0) REVERT: G 88 ASP cc_start: 0.8423 (t0) cc_final: 0.8217 (t0) REVERT: G 103 GLN cc_start: 0.9120 (mp10) cc_final: 0.8753 (mp10) REVERT: H 14 GLU cc_start: 0.8906 (tp30) cc_final: 0.8362 (tp30) REVERT: H 103 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: H 134 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7652 (mm-40) REVERT: F 117 GLU cc_start: 0.8479 (pp20) cc_final: 0.8231 (pp20) REVERT: F 123 LYS cc_start: 0.9142 (tttp) cc_final: 0.8869 (ttmm) outliers start: 106 outliers final: 36 residues processed: 698 average time/residue: 1.3352 time to fit residues: 1046.1696 Evaluate side-chains 638 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 595 time to evaluate : 2.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 9 LEU 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 75 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 497 LEU 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 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 T residue 103 GLN 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 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 X residue 486 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 137 VAL 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 163 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.0070 overall best weight: 2.0004 ------------------------------------------------------------------------------- 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 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 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.099653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.069782 restraints weight = 50048.856| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.28 r_work: 0.2712 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20223 Z= 0.188 Angle : 0.613 7.305 27351 Z= 0.317 Chirality : 0.045 0.171 2905 Planarity : 0.003 0.037 3638 Dihedral : 4.662 56.201 2706 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.47 % Allowed : 26.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2415 helix: 2.50 (0.20), residues: 614 sheet: 0.07 (0.18), residues: 722 loop : 1.11 (0.23), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.007 0.001 HIS E 79 PHE 0.017 0.002 PHE F 15 TYR 0.018 0.001 TYR F 20 ARG 0.009 0.001 ARG D 17 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 930) hydrogen bonds : angle 4.87890 ( 2691) covalent geometry : bond 0.00437 (20223) covalent geometry : angle 0.61252 (27351) *********************** 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 754 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 636 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8925 (mmtm) REVERT: A 87 ASN cc_start: 0.9209 (m110) cc_final: 0.8836 (m110) REVERT: C 14 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 63 ARG cc_start: 0.9185 (ttm-80) cc_final: 0.8832 (ttp80) REVERT: C 71 THR cc_start: 0.9101 (m) cc_final: 0.8890 (p) REVERT: C 72 ASN cc_start: 0.8432 (t0) cc_final: 0.7738 (t0) REVERT: C 88 ASP cc_start: 0.8493 (t0) cc_final: 0.8108 (t0) REVERT: C 103 GLN cc_start: 0.9036 (mp10) cc_final: 0.8251 (mp10) REVERT: C 117 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 66 MET cc_start: 0.8683 (mmm) cc_final: 0.8477 (mmm) REVERT: B 50 LYS cc_start: 0.8644 (ptmt) cc_final: 0.8291 (pptt) REVERT: B 60 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8645 (mm-30) REVERT: B 63 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8604 (ttm110) REVERT: P 103 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8202 (mm110) REVERT: N 1 MET cc_start: 0.7978 (ptm) cc_final: 0.7728 (ptm) REVERT: N 14 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8138 (tm-30) REVERT: N 62 HIS cc_start: 0.8822 (t-90) cc_final: 0.8603 (t70) REVERT: N 64 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8207 (tmtm) REVERT: N 88 ASP cc_start: 0.8579 (t0) cc_final: 0.8093 (t0) REVERT: N 103 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8700 (mm-40) REVERT: N 117 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8159 (tm-30) REVERT: M 14 GLU cc_start: 0.8833 (tp30) cc_final: 0.8312 (mm-30) REVERT: M 25 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: M 103 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: M 117 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7678 (tm-30) REVERT: O 59 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8858 (mmmm) REVERT: O 60 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8682 (mm-30) REVERT: O 63 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8631 (ttm110) REVERT: T 87 ASN cc_start: 0.9232 (m-40) cc_final: 0.8823 (m110) REVERT: T 103 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8615 (mm110) REVERT: T 134 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8791 (tm-30) REVERT: R 14 GLU cc_start: 0.8849 (tp30) cc_final: 0.8170 (tm-30) REVERT: R 63 ARG cc_start: 0.9251 (mtp85) cc_final: 0.8957 (ttp80) REVERT: R 88 ASP cc_start: 0.8416 (t0) cc_final: 0.8094 (t0) REVERT: R 103 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8590 (mp10) REVERT: R 117 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8065 (tm-30) REVERT: Q 14 GLU cc_start: 0.8815 (tp30) cc_final: 0.8518 (mm-30) REVERT: Q 25 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: Q 66 MET cc_start: 0.9076 (mmm) cc_final: 0.8866 (mmm) REVERT: Q 71 THR cc_start: 0.9135 (t) cc_final: 0.8644 (p) REVERT: Q 100 ASN cc_start: 0.7941 (t0) cc_final: 0.7612 (t0) REVERT: Q 103 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: Q 134 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8373 (tm-30) REVERT: S 50 LYS cc_start: 0.8437 (pttm) cc_final: 0.8160 (pptt) REVERT: S 63 ARG cc_start: 0.8855 (ttp-110) cc_final: 0.8609 (ttm110) REVERT: S 87 ASN cc_start: 0.9263 (m-40) cc_final: 0.9000 (m-40) REVERT: X 484 GLU cc_start: 0.8876 (mp0) cc_final: 0.8529 (mp0) REVERT: E 68 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8715 (mm-40) REVERT: E 103 GLN cc_start: 0.8643 (mt0) cc_final: 0.8407 (mm110) REVERT: G 72 ASN cc_start: 0.8784 (t0) cc_final: 0.8143 (t0) REVERT: G 87 ASN cc_start: 0.8689 (t0) cc_final: 0.8169 (t0) REVERT: G 88 ASP cc_start: 0.8508 (t0) cc_final: 0.8223 (t0) REVERT: G 101 ASN cc_start: 0.8974 (m-40) cc_final: 0.8699 (m-40) REVERT: G 103 GLN cc_start: 0.9161 (mp10) cc_final: 0.8728 (mp10) REVERT: G 117 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7890 (tm-30) REVERT: H 14 GLU cc_start: 0.8908 (tp30) cc_final: 0.8400 (tp30) REVERT: H 103 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7661 (mp10) REVERT: H 134 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7737 (mm-40) REVERT: F 107 ARG cc_start: 0.8807 (mtt180) cc_final: 0.8450 (mtt180) REVERT: F 117 GLU cc_start: 0.8536 (pp20) cc_final: 0.8324 (pp20) outliers start: 118 outliers final: 62 residues processed: 700 average time/residue: 1.2519 time to fit residues: 987.0508 Evaluate side-chains 672 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 602 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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 D residue 9 LEU 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 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 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 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 T residue 103 GLN Chi-restraints excluded: chain R residue 1 MET 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 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 474 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain G residue 71 THR 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 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 J residue 486 LEU Chi-restraints excluded: chain J residue 502 ASP Chi-restraints excluded: chain W residue 485 SER 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 143 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 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 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 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** ** 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** S 24 ASN 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.102163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073397 restraints weight = 50199.472| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.15 r_work: 0.2754 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20223 Z= 0.141 Angle : 0.609 9.955 27351 Z= 0.310 Chirality : 0.044 0.168 2905 Planarity : 0.003 0.038 3638 Dihedral : 4.454 43.700 2706 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.01 % Allowed : 28.37 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.18), residues: 2415 helix: 2.24 (0.20), residues: 644 sheet: 0.14 (0.19), residues: 714 loop : 1.22 (0.23), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 509 HIS 0.006 0.001 HIS E 79 PHE 0.015 0.002 PHE N 131 TYR 0.017 0.001 TYR F 20 ARG 0.009 0.001 ARG M 17 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 930) hydrogen bonds : angle 4.75503 ( 2691) covalent geometry : bond 0.00323 (20223) covalent geometry : angle 0.60856 (27351) *********************** 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 753 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 645 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8858 (mmtm) REVERT: A 87 ASN cc_start: 0.9193 (m110) cc_final: 0.8731 (m110) REVERT: A 103 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8576 (mp10) REVERT: C 14 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8076 (tm-30) REVERT: C 63 ARG cc_start: 0.9155 (ttm-80) cc_final: 0.8812 (ttp80) REVERT: C 71 THR cc_start: 0.9086 (m) cc_final: 0.8807 (p) REVERT: C 72 ASN cc_start: 0.8436 (t0) cc_final: 0.7708 (t0) REVERT: C 88 ASP cc_start: 0.8528 (t0) cc_final: 0.8106 (t0) REVERT: C 103 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8573 (mm-40) REVERT: C 107 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7832 (mtp180) REVERT: C 117 GLU cc_start: 0.8515 (tm-30) cc_final: 0.7959 (tm-30) REVERT: D 25 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: D 66 MET cc_start: 0.8682 (mmm) cc_final: 0.8475 (mmm) REVERT: B 50 LYS cc_start: 0.8611 (ptmt) cc_final: 0.8243 (pptt) REVERT: B 59 LYS cc_start: 0.9214 (mmmm) cc_final: 0.8888 (mmmm) REVERT: B 63 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8608 (ttm110) REVERT: L 500 GLU cc_start: 0.8220 (tt0) cc_final: 0.7997 (tt0) REVERT: P 103 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8209 (mm110) REVERT: N 14 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8050 (tm-30) REVERT: N 62 HIS cc_start: 0.8816 (t-90) cc_final: 0.8597 (t70) REVERT: N 88 ASP cc_start: 0.8575 (t0) cc_final: 0.8073 (t0) REVERT: N 103 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8738 (mm-40) REVERT: N 117 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8158 (tm-30) REVERT: M 14 GLU cc_start: 0.8758 (tp30) cc_final: 0.8301 (mm-30) REVERT: M 17 ARG cc_start: 0.8990 (ttp80) cc_final: 0.8738 (ttp80) REVERT: M 25 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: M 59 LYS cc_start: 0.9141 (tttm) cc_final: 0.8870 (tttm) REVERT: M 103 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: M 117 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7628 (tm-30) REVERT: O 37 ASN cc_start: 0.8430 (m110) cc_final: 0.8053 (OUTLIER) REVERT: O 59 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8812 (mmmm) REVERT: O 63 ARG cc_start: 0.8836 (ttp-110) cc_final: 0.8609 (ttm110) REVERT: O 107 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8644 (mtp85) REVERT: T 87 ASN cc_start: 0.9190 (m-40) cc_final: 0.8895 (m-40) REVERT: T 103 GLN cc_start: 0.8760 (mt0) cc_final: 0.8515 (mm110) REVERT: T 134 GLN cc_start: 0.8994 (tm-30) cc_final: 0.8717 (tm-30) REVERT: R 88 ASP cc_start: 0.8423 (t0) cc_final: 0.8016 (t0) REVERT: R 103 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8520 (mp10) REVERT: R 117 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8005 (tm-30) REVERT: Q 25 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: Q 66 MET cc_start: 0.9080 (mmm) cc_final: 0.8850 (mmm) REVERT: Q 71 THR cc_start: 0.9081 (t) cc_final: 0.8609 (p) REVERT: Q 103 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: Q 117 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7372 (pp20) REVERT: S 50 LYS cc_start: 0.8397 (pttm) cc_final: 0.8131 (pptt) REVERT: S 63 ARG cc_start: 0.8841 (ttp-110) cc_final: 0.8587 (ttm110) REVERT: X 484 GLU cc_start: 0.8890 (mp0) cc_final: 0.8603 (mp0) REVERT: E 68 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8649 (mm-40) REVERT: E 103 GLN cc_start: 0.8600 (mt0) cc_final: 0.8378 (mm110) REVERT: G 72 ASN cc_start: 0.8772 (t0) cc_final: 0.8121 (t0) REVERT: G 87 ASN cc_start: 0.8635 (t0) cc_final: 0.8077 (t0) REVERT: G 88 ASP cc_start: 0.8485 (t0) cc_final: 0.8151 (t0) REVERT: G 101 ASN cc_start: 0.9153 (m-40) cc_final: 0.8708 (m110) REVERT: G 103 GLN cc_start: 0.9171 (mp10) cc_final: 0.8316 (mp10) REVERT: H 14 GLU cc_start: 0.8831 (tp30) cc_final: 0.8376 (tp30) REVERT: H 103 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: H 123 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8610 (ttmt) REVERT: F 25 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8505 (mm110) REVERT: F 59 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8788 (mmmm) REVERT: F 107 ARG cc_start: 0.8841 (mtt180) cc_final: 0.8551 (mtt180) REVERT: F 117 GLU cc_start: 0.8518 (pp20) cc_final: 0.8313 (pp20) REVERT: F 123 LYS cc_start: 0.9081 (tttp) cc_final: 0.8837 (tttp) outliers start: 108 outliers final: 57 residues processed: 704 average time/residue: 1.3379 time to fit residues: 1060.2562 Evaluate side-chains 665 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 598 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 67 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 75 THR 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 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 107 ARG 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 67 SER Chi-restraints excluded: chain R residue 1 MET 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 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 75 THR 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 G residue 67 SER Chi-restraints excluded: chain G residue 71 THR 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 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 502 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 0.0570 chunk 104 optimal weight: 3.9990 chunk 25 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.4280 ------------------------------------------------------------------------------- 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 A 69 ASN C 58 GLN C 68 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 93 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 GLN ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.101797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.072716 restraints weight = 54364.469| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.28 r_work: 0.2735 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20223 Z= 0.156 Angle : 0.622 8.999 27351 Z= 0.316 Chirality : 0.045 0.169 2905 Planarity : 0.004 0.039 3638 Dihedral : 4.332 34.700 2704 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.33 % Allowed : 29.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.18), residues: 2415 helix: 2.44 (0.20), residues: 624 sheet: 0.11 (0.18), residues: 722 loop : 1.19 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 509 HIS 0.006 0.001 HIS E 79 PHE 0.016 0.002 PHE F 15 TYR 0.018 0.001 TYR F 20 ARG 0.010 0.001 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 930) hydrogen bonds : angle 4.72318 ( 2691) covalent geometry : bond 0.00360 (20223) covalent geometry : angle 0.62197 (27351) *********************** 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 750 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 635 time to evaluate : 2.172 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: 0.9223 (ttmt) cc_final: 0.8893 (mmtm) REVERT: A 87 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8721 (m110) REVERT: A 103 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8580 (mp10) REVERT: C 14 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8123 (tm-30) REVERT: C 63 ARG cc_start: 0.9163 (ttm-80) cc_final: 0.8826 (ttp80) REVERT: C 71 THR cc_start: 0.9091 (m) cc_final: 0.8786 (p) REVERT: C 72 ASN cc_start: 0.8475 (t0) cc_final: 0.7720 (t0) REVERT: C 88 ASP cc_start: 0.8604 (t0) cc_final: 0.8122 (t0) REVERT: C 103 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8584 (mm-40) REVERT: C 107 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (mtp180) REVERT: C 117 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7988 (tm-30) REVERT: D 14 GLU cc_start: 0.8979 (tp30) cc_final: 0.8769 (tp30) REVERT: D 17 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8759 (ttp80) REVERT: D 25 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 50 LYS cc_start: 0.8604 (ptmt) cc_final: 0.8262 (pptt) REVERT: B 59 LYS cc_start: 0.9232 (mmmm) cc_final: 0.8900 (mmmm) REVERT: B 63 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8623 (ttm110) REVERT: L 500 GLU cc_start: 0.8300 (tt0) cc_final: 0.8083 (tt0) REVERT: N 14 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8075 (tm-30) REVERT: N 88 ASP cc_start: 0.8605 (t0) cc_final: 0.8116 (t0) REVERT: N 103 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8834 (mm-40) REVERT: N 109 MET cc_start: 0.8989 (mtt) cc_final: 0.8422 (mtt) REVERT: N 117 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8144 (tm-30) REVERT: M 14 GLU cc_start: 0.8820 (tp30) cc_final: 0.8173 (mm-30) REVERT: M 17 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8795 (ttp80) REVERT: M 25 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: M 95 MET cc_start: 0.9021 (mtt) cc_final: 0.8503 (mtp) REVERT: M 103 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: M 117 GLU cc_start: 0.8460 (tm-30) cc_final: 0.7619 (tm-30) REVERT: O 37 ASN cc_start: 0.8475 (m110) cc_final: 0.8140 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8565 (pptt) cc_final: 0.8100 (pptt) REVERT: O 59 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8839 (mmmm) REVERT: O 60 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8676 (mm-30) REVERT: O 63 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8656 (ttm110) REVERT: T 87 ASN cc_start: 0.9186 (m-40) cc_final: 0.8890 (m110) REVERT: T 103 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8526 (mm110) REVERT: T 134 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8835 (tm-30) REVERT: R 14 GLU cc_start: 0.8864 (tp30) cc_final: 0.8181 (tm-30) REVERT: R 60 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: R 63 ARG cc_start: 0.9303 (ttm110) cc_final: 0.8819 (ttp-110) REVERT: R 88 ASP cc_start: 0.8514 (t0) cc_final: 0.8083 (t0) REVERT: R 103 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8656 (mp10) REVERT: R 107 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7492 (ttm170) REVERT: R 117 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8013 (tm-30) REVERT: Q 14 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8549 (tp30) REVERT: Q 25 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: Q 59 LYS cc_start: 0.9150 (tttm) cc_final: 0.8942 (tttm) REVERT: Q 66 MET cc_start: 0.9101 (mmm) cc_final: 0.8872 (mmm) REVERT: Q 71 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8636 (p) REVERT: Q 103 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: Q 117 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: S 50 LYS cc_start: 0.8407 (pttm) cc_final: 0.8151 (pptt) REVERT: S 59 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8916 (mmmm) REVERT: S 63 ARG cc_start: 0.8899 (ttp-110) cc_final: 0.8643 (ttm110) REVERT: S 107 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8723 (mtp85) REVERT: X 484 GLU cc_start: 0.8883 (mp0) cc_final: 0.8602 (mp0) REVERT: E 68 GLN cc_start: 0.9023 (mm-40) cc_final: 0.8738 (mm-40) REVERT: E 103 GLN cc_start: 0.8671 (mt0) cc_final: 0.8460 (mm110) REVERT: G 64 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8165 (tmtm) REVERT: G 72 ASN cc_start: 0.8774 (t0) cc_final: 0.8150 (t0) REVERT: G 87 ASN cc_start: 0.8661 (t0) cc_final: 0.8100 (t0) REVERT: G 88 ASP cc_start: 0.8504 (t0) cc_final: 0.8143 (t0) REVERT: G 101 ASN cc_start: 0.9234 (m-40) cc_final: 0.8687 (m110) REVERT: G 103 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8300 (mp10) REVERT: G 107 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: H 59 LYS cc_start: 0.9118 (tttm) cc_final: 0.8908 (tttm) REVERT: H 103 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7681 (mp10) REVERT: H 123 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8628 (ttmt) REVERT: H 134 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7756 (mm110) REVERT: F 59 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8952 (mmmm) REVERT: F 107 ARG cc_start: 0.8882 (mtt180) cc_final: 0.8547 (mtt180) REVERT: F 117 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8379 (pp20) REVERT: F 123 LYS cc_start: 0.9098 (tttp) cc_final: 0.8866 (tttp) outliers start: 115 outliers final: 64 residues processed: 692 average time/residue: 1.3314 time to fit residues: 1033.4583 Evaluate side-chains 694 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 613 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 68 GLN 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 D residue 92 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 86 LEU 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 137 VAL 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 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 67 SER Chi-restraints excluded: chain T residue 103 GLN Chi-restraints excluded: chain R residue 1 MET 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 R residue 114 LEU 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 71 THR 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 75 THR Chi-restraints excluded: chain S residue 107 ARG Chi-restraints excluded: chain S residue 114 LEU 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 64 LYS 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 117 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain K residue 492 THR Chi-restraints excluded: chain W residue 485 SER Chi-restraints excluded: chain U residue 505 THR Chi-restraints excluded: chain I residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 130 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN P 134 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN ** S 134 GLN ** 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 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 = 0.3312 r_free = 0.3312 target = 0.097026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.066585 restraints weight = 53620.320| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 4.35 r_work: 0.2598 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 20223 Z= 0.288 Angle : 0.689 10.185 27351 Z= 0.350 Chirality : 0.048 0.195 2905 Planarity : 0.004 0.038 3638 Dihedral : 4.751 39.030 2704 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.98 % Allowed : 28.74 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.18), residues: 2415 helix: 2.29 (0.20), residues: 624 sheet: 0.01 (0.18), residues: 722 loop : 1.14 (0.22), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 509 HIS 0.005 0.001 HIS E 79 PHE 0.021 0.002 PHE H 15 TYR 0.021 0.002 TYR F 20 ARG 0.012 0.001 ARG H 17 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 930) hydrogen bonds : angle 4.96275 ( 2691) covalent geometry : bond 0.00673 (20223) covalent geometry : angle 0.68887 (27351) *********************** 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 748 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 619 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8843 (mmpt) REVERT: A 87 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8560 (m110) REVERT: A 117 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7622 (tp30) REVERT: C 14 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8058 (tm-30) REVERT: C 63 ARG cc_start: 0.9198 (ttm-80) cc_final: 0.8880 (ttp80) REVERT: C 71 THR cc_start: 0.8970 (m) cc_final: 0.8606 (p) REVERT: C 72 ASN cc_start: 0.8290 (t0) cc_final: 0.7508 (t0) REVERT: C 88 ASP cc_start: 0.8702 (t0) cc_final: 0.8266 (t0) REVERT: C 103 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8546 (mm-40) REVERT: C 107 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7879 (mtp180) REVERT: C 117 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 17 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8719 (ttp80) REVERT: D 25 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: B 50 LYS cc_start: 0.8489 (ptmt) cc_final: 0.8289 (ptmt) REVERT: B 59 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8927 (mmmm) REVERT: B 63 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8644 (ttm110) REVERT: P 13 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8160 (mtm110) REVERT: P 103 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: N 14 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8014 (tm-30) REVERT: N 88 ASP cc_start: 0.8683 (t0) cc_final: 0.8210 (t0) REVERT: N 103 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8573 (mp10) REVERT: N 117 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8136 (tm-30) REVERT: M 14 GLU cc_start: 0.8776 (tp30) cc_final: 0.8108 (mm-30) REVERT: M 17 ARG cc_start: 0.8963 (ttp80) cc_final: 0.8701 (ttp80) REVERT: M 25 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: M 103 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: M 117 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7636 (tm-30) REVERT: O 22 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8334 (tm) REVERT: O 37 ASN cc_start: 0.8566 (m110) cc_final: 0.8212 (OUTLIER) REVERT: O 59 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8860 (mmmm) REVERT: O 63 ARG cc_start: 0.8856 (ttp-110) cc_final: 0.8612 (ttm110) REVERT: T 87 ASN cc_start: 0.9138 (m-40) cc_final: 0.8691 (m110) REVERT: T 103 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8531 (mm110) REVERT: R 14 GLU cc_start: 0.8798 (tp30) cc_final: 0.8048 (tm-30) REVERT: R 63 ARG cc_start: 0.9349 (ttm110) cc_final: 0.8806 (ttp80) REVERT: R 88 ASP cc_start: 0.8607 (t0) cc_final: 0.8195 (t0) REVERT: R 103 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8675 (mp10) REVERT: R 117 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8165 (tm-30) REVERT: Q 14 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8449 (tp30) REVERT: Q 17 ARG cc_start: 0.8955 (ttp80) cc_final: 0.8679 (ttp80) REVERT: Q 25 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: Q 71 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8455 (p) REVERT: Q 100 ASN cc_start: 0.7816 (t0) cc_final: 0.7521 (t0) REVERT: Q 103 GLN cc_start: 0.8167 (mp10) cc_final: 0.7665 (mp10) REVERT: S 50 LYS cc_start: 0.8268 (pttm) cc_final: 0.8013 (pptt) REVERT: S 59 LYS cc_start: 0.9243 (mmmm) cc_final: 0.8983 (mmmm) REVERT: S 63 ARG cc_start: 0.8866 (ttp-110) cc_final: 0.8634 (ttm110) REVERT: X 484 GLU cc_start: 0.8835 (mp0) cc_final: 0.8541 (mp0) REVERT: E 68 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8667 (mm-40) REVERT: E 103 GLN cc_start: 0.8620 (mt0) cc_final: 0.8394 (mm110) REVERT: G 14 GLU cc_start: 0.8789 (tp30) cc_final: 0.7983 (tm-30) REVERT: G 64 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8171 (tmtm) REVERT: G 72 ASN cc_start: 0.8634 (t0) cc_final: 0.8042 (t0) REVERT: G 87 ASN cc_start: 0.8778 (t0) cc_final: 0.8222 (t0) REVERT: G 88 ASP cc_start: 0.8642 (t0) cc_final: 0.8313 (t0) REVERT: G 101 ASN cc_start: 0.9216 (m-40) cc_final: 0.8679 (m-40) REVERT: G 103 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: G 106 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7403 (mtp180) REVERT: G 107 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7581 (mtm-85) REVERT: H 25 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8218 (mt0) REVERT: H 103 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: H 134 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7946 (mm110) REVERT: F 22 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8407 (tm) REVERT: F 59 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8930 (mmmm) REVERT: F 117 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (pp20) REVERT: F 123 LYS cc_start: 0.9035 (tttp) cc_final: 0.8803 (tttp) outliers start: 129 outliers final: 72 residues processed: 689 average time/residue: 1.3719 time to fit residues: 1056.9894 Evaluate side-chains 684 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 593 time to evaluate : 2.118 ------------------------------------------------------------------------------- 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 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 114 LEU 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 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 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 22 LEU 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 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 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 R residue 105 LEU 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 71 THR Chi-restraints excluded: chain Q residue 94 VAL 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 X residue 486 LEU 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 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 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 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 F residue 114 LEU Chi-restraints excluded: chain F residue 117 GLU Chi-restraints excluded: chain J residue 502 ASP 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 100 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 GLN N 58 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN T 68 GLN T 134 GLN R 58 GLN ** R 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.072063 restraints weight = 48834.140| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.09 r_work: 0.2720 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 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 = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20223 Z= 0.159 Angle : 0.669 11.253 27351 Z= 0.335 Chirality : 0.045 0.169 2905 Planarity : 0.004 0.043 3638 Dihedral : 4.409 34.422 2702 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.15 % Allowed : 29.76 % Favored : 65.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.18), residues: 2415 helix: 2.39 (0.20), residues: 624 sheet: 0.03 (0.18), residues: 722 loop : 1.18 (0.22), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 509 HIS 0.006 0.001 HIS E 79 PHE 0.016 0.002 PHE O 15 TYR 0.017 0.001 TYR F 20 ARG 0.010 0.001 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 930) hydrogen bonds : angle 4.80960 ( 2691) covalent geometry : bond 0.00371 (20223) covalent geometry : angle 0.66866 (27351) *********************** 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 746 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 635 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8867 (mmpt) REVERT: A 87 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8692 (m110) REVERT: A 103 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8562 (mp10) REVERT: C 14 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 63 ARG cc_start: 0.9170 (ttm-80) cc_final: 0.8857 (ttp80) REVERT: C 71 THR cc_start: 0.8988 (m) cc_final: 0.8598 (p) REVERT: C 72 ASN cc_start: 0.8327 (t0) cc_final: 0.7528 (t0) REVERT: C 88 ASP cc_start: 0.8706 (t0) cc_final: 0.8219 (t0) REVERT: C 103 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8592 (mm-40) REVERT: C 107 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7958 (mtm180) REVERT: C 117 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 14 GLU cc_start: 0.8953 (tp30) cc_final: 0.8680 (tp30) REVERT: D 17 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8740 (ttp80) REVERT: D 25 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: B 50 LYS cc_start: 0.8540 (ptmt) cc_final: 0.8214 (pptt) REVERT: B 59 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8918 (mmmm) REVERT: B 63 ARG cc_start: 0.8858 (ttp-110) cc_final: 0.8629 (ttm110) REVERT: P 103 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8434 (mt0) REVERT: N 14 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7996 (tm-30) REVERT: N 88 ASP cc_start: 0.8627 (t0) cc_final: 0.8130 (t0) REVERT: N 103 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8628 (mm-40) REVERT: N 117 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 14 GLU cc_start: 0.8767 (tp30) cc_final: 0.8086 (mm-30) REVERT: M 17 ARG cc_start: 0.8982 (ttp80) cc_final: 0.8760 (ttp80) REVERT: M 25 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: M 95 MET cc_start: 0.8947 (mtt) cc_final: 0.8618 (mtp) REVERT: M 103 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: M 117 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7558 (tm-30) REVERT: O 37 ASN cc_start: 0.8511 (m110) cc_final: 0.8193 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8452 (pptt) cc_final: 0.7990 (pptt) REVERT: O 59 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8874 (mmmm) REVERT: O 63 ARG cc_start: 0.8858 (ttp-110) cc_final: 0.8629 (ttm110) REVERT: T 87 ASN cc_start: 0.9158 (m-40) cc_final: 0.8872 (m110) REVERT: T 103 GLN cc_start: 0.8727 (mt0) cc_final: 0.8480 (mm110) REVERT: T 134 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8790 (tm130) REVERT: R 14 GLU cc_start: 0.8801 (tp30) cc_final: 0.8113 (tm-30) REVERT: R 60 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: R 63 ARG cc_start: 0.9312 (ttm110) cc_final: 0.8767 (ttp80) REVERT: R 88 ASP cc_start: 0.8582 (t0) cc_final: 0.8176 (t0) REVERT: R 103 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8663 (mp10) REVERT: R 117 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8090 (tm-30) REVERT: Q 14 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8494 (mm-30) REVERT: Q 17 ARG cc_start: 0.8939 (ttp80) cc_final: 0.8678 (ttp80) REVERT: Q 25 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: Q 71 THR cc_start: 0.9011 (OUTLIER) cc_final: 0.8536 (p) REVERT: Q 100 ASN cc_start: 0.7898 (t0) cc_final: 0.7589 (t0) REVERT: Q 103 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: S 50 LYS cc_start: 0.8293 (pttm) cc_final: 0.8050 (pptt) REVERT: S 59 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8925 (mmmm) REVERT: S 63 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8658 (ttm110) REVERT: X 484 GLU cc_start: 0.8854 (mp0) cc_final: 0.8549 (mp0) REVERT: E 68 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8601 (mm-40) REVERT: E 103 GLN cc_start: 0.8591 (mt0) cc_final: 0.8384 (mm110) REVERT: G 3 MET cc_start: 0.8518 (mmp) cc_final: 0.8247 (mmm) REVERT: G 64 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8172 (tmtm) REVERT: G 72 ASN cc_start: 0.8703 (t0) cc_final: 0.8102 (t0) REVERT: G 87 ASN cc_start: 0.8680 (t0) cc_final: 0.8106 (t0) REVERT: G 88 ASP cc_start: 0.8575 (t0) cc_final: 0.8186 (t0) REVERT: G 101 ASN cc_start: 0.9291 (m-40) cc_final: 0.8697 (m110) REVERT: G 103 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: G 106 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7429 (mtp180) REVERT: G 107 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7573 (mtm-85) REVERT: H 14 GLU cc_start: 0.8901 (tp30) cc_final: 0.8484 (tp30) REVERT: H 17 ARG cc_start: 0.9047 (ttp80) cc_final: 0.8587 (ttp80) REVERT: H 103 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: H 117 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: F 59 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8909 (mmmm) REVERT: F 117 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8362 (pp20) REVERT: F 123 LYS cc_start: 0.9068 (tttp) cc_final: 0.8847 (tttp) outliers start: 111 outliers final: 69 residues processed: 689 average time/residue: 1.3808 time to fit residues: 1074.9643 Evaluate side-chains 692 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 605 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 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 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 67 SER Chi-restraints excluded: chain P residue 95 MET 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 39 SER 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 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 67 SER 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 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 THR 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 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 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 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 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 117 GLU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 502 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 221 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 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 103 GLN T 134 GLN R 58 GLN R 68 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** 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** F 25 GLN F 68 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.100726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.071633 restraints weight = 45653.370| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 4.11 r_work: 0.2738 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20223 Z= 0.146 Angle : 0.681 11.433 27351 Z= 0.338 Chirality : 0.045 0.194 2905 Planarity : 0.004 0.044 3638 Dihedral : 4.322 33.610 2702 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.78 % Allowed : 30.78 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.18), residues: 2415 helix: 2.41 (0.20), residues: 624 sheet: 0.06 (0.18), residues: 722 loop : 1.19 (0.22), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP I 509 HIS 0.005 0.000 HIS E 79 PHE 0.016 0.002 PHE R 131 TYR 0.018 0.001 TYR C 20 ARG 0.011 0.001 ARG H 63 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 930) hydrogen bonds : angle 4.74061 ( 2691) covalent geometry : bond 0.00339 (20223) covalent geometry : angle 0.68056 (27351) *********************** 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 733 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 630 time to evaluate : 2.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9229 (ttmt) cc_final: 0.8827 (mmpt) REVERT: A 87 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8745 (m110) REVERT: A 103 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8543 (mp10) REVERT: C 14 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 63 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8843 (ttp80) REVERT: C 71 THR cc_start: 0.8969 (m) cc_final: 0.8584 (p) REVERT: C 72 ASN cc_start: 0.8323 (t0) cc_final: 0.7520 (t0) REVERT: C 88 ASP cc_start: 0.8706 (t0) cc_final: 0.8193 (t0) REVERT: C 103 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: C 117 GLU cc_start: 0.8578 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 14 GLU cc_start: 0.8939 (tp30) cc_final: 0.8716 (tp30) REVERT: D 25 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: B 50 LYS cc_start: 0.8583 (ptmt) cc_final: 0.8251 (pptt) REVERT: B 59 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8886 (mmmm) REVERT: B 63 ARG cc_start: 0.8861 (ttp-110) cc_final: 0.8599 (ttm110) REVERT: L 500 GLU cc_start: 0.8226 (tt0) cc_final: 0.7996 (tt0) REVERT: P 103 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: N 3 MET cc_start: 0.8555 (mmm) cc_final: 0.8308 (tpp) REVERT: N 14 GLU cc_start: 0.8638 (tm-30) cc_final: 0.7983 (tm-30) REVERT: N 88 ASP cc_start: 0.8610 (t0) cc_final: 0.8103 (t0) REVERT: N 103 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8750 (mm-40) REVERT: N 117 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8112 (tm-30) REVERT: M 14 GLU cc_start: 0.8771 (tp30) cc_final: 0.8117 (mm-30) REVERT: M 17 ARG cc_start: 0.8999 (ttp80) cc_final: 0.8777 (ttp80) REVERT: M 25 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8106 (mp10) REVERT: M 95 MET cc_start: 0.8992 (mtt) cc_final: 0.8607 (mtp) REVERT: M 103 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: M 117 GLU cc_start: 0.8488 (tm-30) cc_final: 0.7571 (tm-30) REVERT: O 37 ASN cc_start: 0.8491 (m110) cc_final: 0.8198 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8528 (pptt) cc_final: 0.8056 (pptt) REVERT: O 53 ASP cc_start: 0.9131 (m-30) cc_final: 0.8729 (m-30) REVERT: O 59 LYS cc_start: 0.9230 (mmmm) cc_final: 0.8876 (mmmm) REVERT: O 60 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8645 (mm-30) REVERT: O 63 ARG cc_start: 0.8882 (ttp-110) cc_final: 0.8637 (ttm110) REVERT: O 107 ARG cc_start: 0.8816 (mtt90) cc_final: 0.8315 (mtt180) REVERT: T 87 ASN cc_start: 0.9170 (m-40) cc_final: 0.8921 (m110) REVERT: T 95 MET cc_start: 0.9271 (mtp) cc_final: 0.9044 (mtp) REVERT: T 103 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8487 (mm110) REVERT: T 134 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8723 (tm130) REVERT: R 14 GLU cc_start: 0.8826 (tp30) cc_final: 0.8133 (tm-30) REVERT: R 60 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: R 63 ARG cc_start: 0.9306 (ttm110) cc_final: 0.8767 (ttp80) REVERT: R 88 ASP cc_start: 0.8573 (t0) cc_final: 0.8145 (t0) REVERT: R 103 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8634 (mp10) REVERT: R 117 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Q 14 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8408 (mm-30) REVERT: Q 17 ARG cc_start: 0.8929 (ttp80) cc_final: 0.8529 (ttp80) REVERT: Q 25 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: Q 71 THR cc_start: 0.8988 (t) cc_final: 0.8522 (p) REVERT: Q 103 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: Q 117 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7352 (pp20) REVERT: S 50 LYS cc_start: 0.8311 (pttm) cc_final: 0.8057 (pptt) REVERT: S 59 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8941 (mmmm) REVERT: X 484 GLU cc_start: 0.8848 (mp0) cc_final: 0.8533 (mp0) REVERT: E 68 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8627 (mm-40) REVERT: E 103 GLN cc_start: 0.8603 (mt0) cc_final: 0.8379 (mm110) REVERT: G 64 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8169 (tmtm) REVERT: G 72 ASN cc_start: 0.8704 (t0) cc_final: 0.8101 (t0) REVERT: G 87 ASN cc_start: 0.8657 (t0) cc_final: 0.8075 (t0) REVERT: G 88 ASP cc_start: 0.8573 (t0) cc_final: 0.8173 (t0) REVERT: G 101 ASN cc_start: 0.9297 (m-40) cc_final: 0.8641 (m110) REVERT: G 103 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: H 14 GLU cc_start: 0.8936 (tp30) cc_final: 0.8711 (tp30) REVERT: H 17 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8755 (ttp80) REVERT: H 103 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: H 117 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: F 59 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8909 (mmmm) REVERT: F 60 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8628 (mm-30) REVERT: F 117 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8355 (pp20) REVERT: F 123 LYS cc_start: 0.9047 (tttp) cc_final: 0.8830 (tttp) outliers start: 103 outliers final: 66 residues processed: 682 average time/residue: 1.3527 time to fit residues: 1033.2827 Evaluate side-chains 696 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 614 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 92 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 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER 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 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 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 67 SER 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 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 114 LEU 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 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 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 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 117 GLU 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 505 THR Chi-restraints excluded: chain I residue 485 SER Chi-restraints excluded: chain I residue 492 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 204 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 223 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 185 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 210 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 68 GLN D 122 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 103 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 103 GLN T 134 GLN R 58 GLN ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 GLN F 68 GLN F 134 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.073274 restraints weight = 51978.019| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.24 r_work: 0.2742 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20223 Z= 0.148 Angle : 0.701 11.787 27351 Z= 0.346 Chirality : 0.045 0.179 2905 Planarity : 0.004 0.046 3638 Dihedral : 4.296 33.416 2702 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.64 % Allowed : 31.66 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2415 helix: 2.42 (0.20), residues: 624 sheet: -0.02 (0.18), residues: 772 loop : 1.39 (0.23), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP W 509 HIS 0.005 0.000 HIS E 79 PHE 0.015 0.002 PHE N 131 TYR 0.018 0.001 TYR F 20 ARG 0.012 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 930) hydrogen bonds : angle 4.71318 ( 2691) covalent geometry : bond 0.00346 (20223) covalent geometry : angle 0.70133 (27351) *********************** 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 717 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 617 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9198 (ttmt) cc_final: 0.8815 (mmpt) REVERT: A 87 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8749 (m110) REVERT: A 103 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8522 (mp10) REVERT: C 14 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 63 ARG cc_start: 0.9158 (ttm-80) cc_final: 0.8838 (ttp80) REVERT: C 71 THR cc_start: 0.8971 (m) cc_final: 0.8586 (p) REVERT: C 72 ASN cc_start: 0.8315 (t0) cc_final: 0.7564 (t0) REVERT: C 88 ASP cc_start: 0.8716 (t0) cc_final: 0.8215 (t0) REVERT: C 103 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: C 117 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 14 GLU cc_start: 0.8961 (tp30) cc_final: 0.8694 (tp30) REVERT: D 25 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: B 50 LYS cc_start: 0.8582 (ptmt) cc_final: 0.8247 (pptt) REVERT: B 59 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8873 (mmmm) REVERT: L 500 GLU cc_start: 0.8197 (tt0) cc_final: 0.7954 (tt0) REVERT: P 103 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8357 (mt0) REVERT: N 3 MET cc_start: 0.8540 (mmm) cc_final: 0.8289 (tpp) REVERT: N 14 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8008 (tm-30) REVERT: N 88 ASP cc_start: 0.8615 (t0) cc_final: 0.8107 (t0) REVERT: N 103 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8783 (mm-40) REVERT: N 117 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8131 (tm-30) REVERT: M 14 GLU cc_start: 0.8783 (tp30) cc_final: 0.8125 (mm-30) REVERT: M 17 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8786 (ttp80) REVERT: M 25 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: M 95 MET cc_start: 0.8955 (mtt) cc_final: 0.8598 (mtp) REVERT: M 103 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: M 117 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7555 (tm-30) REVERT: O 37 ASN cc_start: 0.8477 (m110) cc_final: 0.8186 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8507 (pptt) cc_final: 0.8067 (pptt) REVERT: O 59 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8864 (mmmm) REVERT: O 60 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8650 (mm-30) REVERT: O 63 ARG cc_start: 0.8880 (ttp-110) cc_final: 0.8618 (ttm110) REVERT: T 87 ASN cc_start: 0.9166 (m-40) cc_final: 0.8699 (m110) REVERT: T 103 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8473 (mm-40) REVERT: T 134 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8678 (tm130) REVERT: R 14 GLU cc_start: 0.8791 (tp30) cc_final: 0.8101 (tm-30) REVERT: R 60 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: R 63 ARG cc_start: 0.9319 (ttm110) cc_final: 0.8777 (ttp80) REVERT: R 88 ASP cc_start: 0.8580 (t0) cc_final: 0.8157 (t0) REVERT: R 103 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8600 (mp10) REVERT: R 117 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8089 (tm-30) REVERT: Q 14 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8434 (mm-30) REVERT: Q 25 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: Q 71 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8484 (p) REVERT: Q 103 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: Q 117 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7328 (pp20) REVERT: S 50 LYS cc_start: 0.8292 (pttm) cc_final: 0.8039 (pptt) REVERT: S 59 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8899 (mmmm) REVERT: S 63 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8651 (ttp-110) REVERT: S 87 ASN cc_start: 0.9249 (m-40) cc_final: 0.8902 (m-40) REVERT: S 107 ARG cc_start: 0.8899 (mtp85) cc_final: 0.8492 (mtt180) REVERT: X 484 GLU cc_start: 0.8865 (mp0) cc_final: 0.8560 (mp0) REVERT: E 68 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8630 (mm-40) REVERT: E 103 GLN cc_start: 0.8586 (mt0) cc_final: 0.8359 (mm110) REVERT: G 14 GLU cc_start: 0.8811 (tp30) cc_final: 0.8201 (tm-30) REVERT: G 72 ASN cc_start: 0.8679 (t0) cc_final: 0.8064 (t0) REVERT: G 87 ASN cc_start: 0.8639 (t0) cc_final: 0.8062 (t0) REVERT: G 88 ASP cc_start: 0.8581 (t0) cc_final: 0.8126 (t0) REVERT: G 101 ASN cc_start: 0.9303 (m-40) cc_final: 0.8855 (m110) REVERT: G 103 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8393 (mp10) REVERT: H 14 GLU cc_start: 0.8922 (tp30) cc_final: 0.8649 (tp30) REVERT: H 17 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8665 (ttp80) REVERT: H 68 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: H 103 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: H 117 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7270 (pp20) REVERT: F 59 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8900 (mmmm) REVERT: F 107 ARG cc_start: 0.8788 (mtp85) cc_final: 0.8415 (mtt180) REVERT: F 117 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (pp20) REVERT: F 123 LYS cc_start: 0.9041 (tttp) cc_final: 0.8820 (tttp) REVERT: W 492 THR cc_start: 0.8452 (p) cc_final: 0.8085 (p) outliers start: 100 outliers final: 67 residues processed: 671 average time/residue: 1.3381 time to fit residues: 1005.6847 Evaluate side-chains 693 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 608 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain C residue 103 GLN 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 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 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER 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 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 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 67 SER 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 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 THR 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 63 ARG 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 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 68 GLN 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 117 GLU 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 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 10 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 219 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN C 58 GLN C 62 HIS C 68 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN B 134 GLN ** P 68 GLN ** 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 134 GLN R 58 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN 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 = 0.3360 r_free = 0.3360 target = 0.100756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.071607 restraints weight = 47852.323| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.17 r_work: 0.2732 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2757 r_free = 0.2757 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20223 Z= 0.161 Angle : 0.724 12.313 27351 Z= 0.356 Chirality : 0.046 0.184 2905 Planarity : 0.004 0.059 3638 Dihedral : 4.310 32.753 2702 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.36 % Allowed : 32.04 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2415 helix: 2.38 (0.20), residues: 624 sheet: -0.02 (0.18), residues: 772 loop : 1.39 (0.23), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP K 509 HIS 0.005 0.000 HIS E 79 PHE 0.016 0.002 PHE B 131 TYR 0.019 0.001 TYR F 20 ARG 0.013 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 930) hydrogen bonds : angle 4.72341 ( 2691) covalent geometry : bond 0.00379 (20223) covalent geometry : angle 0.72443 (27351) ********************** 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 708 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 614 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8832 (mmpt) REVERT: A 87 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8770 (m110) REVERT: A 103 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8530 (mp10) REVERT: C 14 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 63 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8823 (ttp80) REVERT: C 71 THR cc_start: 0.8977 (m) cc_final: 0.8594 (p) REVERT: C 72 ASN cc_start: 0.8324 (t0) cc_final: 0.7565 (t0) REVERT: C 88 ASP cc_start: 0.8724 (t0) cc_final: 0.8222 (t0) REVERT: C 103 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: C 117 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7944 (tm-30) REVERT: D 14 GLU cc_start: 0.8994 (tp30) cc_final: 0.8545 (tp30) REVERT: D 17 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8830 (ttp80) REVERT: D 25 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: D 59 LYS cc_start: 0.9014 (tttm) cc_final: 0.8775 (tttm) REVERT: B 50 LYS cc_start: 0.8606 (ptmt) cc_final: 0.8269 (pptt) REVERT: B 59 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8875 (mmmm) REVERT: L 500 GLU cc_start: 0.8216 (tt0) cc_final: 0.7977 (tt0) REVERT: P 103 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8358 (mt0) REVERT: N 3 MET cc_start: 0.8558 (mmm) cc_final: 0.8312 (tpp) REVERT: N 14 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8032 (tm-30) REVERT: N 88 ASP cc_start: 0.8633 (t0) cc_final: 0.8129 (t0) REVERT: N 103 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8808 (mm-40) REVERT: N 117 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8154 (tm-30) REVERT: M 14 GLU cc_start: 0.8815 (tp30) cc_final: 0.8144 (mm-30) REVERT: M 17 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8797 (ttp80) REVERT: M 25 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: M 95 MET cc_start: 0.8946 (mtt) cc_final: 0.8561 (mtp) REVERT: M 103 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7532 (mp10) REVERT: M 117 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7556 (tm-30) REVERT: O 37 ASN cc_start: 0.8474 (m110) cc_final: 0.8206 (OUTLIER) REVERT: O 50 LYS cc_start: 0.8517 (pptt) cc_final: 0.8100 (pptt) REVERT: O 53 ASP cc_start: 0.9114 (m-30) cc_final: 0.8727 (m-30) REVERT: O 59 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8878 (mmmm) REVERT: O 60 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8627 (mm-30) REVERT: O 63 ARG cc_start: 0.8859 (ttp-110) cc_final: 0.8587 (ttm110) REVERT: O 107 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8302 (mtt180) REVERT: V 484 GLU cc_start: 0.8852 (mp0) cc_final: 0.8643 (mp0) REVERT: T 87 ASN cc_start: 0.9156 (m-40) cc_final: 0.8891 (m110) REVERT: T 103 GLN cc_start: 0.8752 (mt0) cc_final: 0.8495 (mm-40) REVERT: T 134 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8501 (tm130) REVERT: R 14 GLU cc_start: 0.8804 (tp30) cc_final: 0.8116 (tm-30) REVERT: R 60 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: R 63 ARG cc_start: 0.9291 (ttm110) cc_final: 0.8748 (ttp80) REVERT: R 88 ASP cc_start: 0.8595 (t0) cc_final: 0.8159 (t0) REVERT: R 103 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8666 (mp10) REVERT: R 117 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8084 (tm-30) REVERT: Q 14 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8430 (mm-30) REVERT: Q 17 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8717 (ttp80) REVERT: Q 25 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7991 (mt0) REVERT: Q 71 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8500 (p) REVERT: Q 103 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: Q 117 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7322 (pp20) REVERT: S 50 LYS cc_start: 0.8288 (pttm) cc_final: 0.8029 (pptt) REVERT: S 59 LYS cc_start: 0.9257 (mmmm) cc_final: 0.8907 (mmmm) REVERT: S 107 ARG cc_start: 0.8924 (mtp85) cc_final: 0.8402 (mtt180) REVERT: X 484 GLU cc_start: 0.8849 (mp0) cc_final: 0.8556 (mp0) REVERT: E 68 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8623 (mm-40) REVERT: E 103 GLN cc_start: 0.8596 (mt0) cc_final: 0.8371 (mm110) REVERT: G 14 GLU cc_start: 0.8823 (tp30) cc_final: 0.8215 (tm-30) REVERT: G 72 ASN cc_start: 0.8679 (t0) cc_final: 0.8072 (t0) REVERT: G 87 ASN cc_start: 0.8657 (t0) cc_final: 0.8081 (t0) REVERT: G 88 ASP cc_start: 0.8575 (t0) cc_final: 0.8125 (t0) REVERT: G 101 ASN cc_start: 0.9299 (m-40) cc_final: 0.8821 (m-40) REVERT: G 103 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8413 (mp10) REVERT: H 14 GLU cc_start: 0.8956 (tp30) cc_final: 0.8738 (tp30) REVERT: H 17 ARG cc_start: 0.9080 (ttp80) cc_final: 0.8750 (ttp80) REVERT: H 103 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: H 117 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: F 59 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8913 (mmmm) REVERT: F 107 ARG cc_start: 0.8778 (mtp85) cc_final: 0.8482 (mtt180) REVERT: F 117 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8364 (pp20) REVERT: F 123 LYS cc_start: 0.9053 (tttp) cc_final: 0.8831 (tttp) REVERT: W 492 THR cc_start: 0.8460 (p) cc_final: 0.8094 (p) outliers start: 94 outliers final: 70 residues processed: 667 average time/residue: 1.3883 time to fit residues: 1040.2544 Evaluate side-chains 695 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 610 time to evaluate : 2.129 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain C residue 103 GLN 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 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 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain P residue 7 SER 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 73 CYS 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 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 67 SER Chi-restraints excluded: chain T residue 134 GLN Chi-restraints excluded: chain R residue 1 MET 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 25 GLN Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 THR 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 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 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 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 117 GLU 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 505 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 183 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 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 134 GLN R 58 GLN R 68 GLN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 GLN G 58 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 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 = 0.3392 r_free = 0.3392 target = 0.101140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.073480 restraints weight = 36853.970| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.63 r_work: 0.2761 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 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 = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20223 Z= 0.180 Angle : 0.735 13.269 27351 Z= 0.361 Chirality : 0.046 0.186 2905 Planarity : 0.004 0.051 3638 Dihedral : 4.359 31.985 2702 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.64 % Allowed : 31.85 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.18), residues: 2415 helix: 2.35 (0.20), residues: 624 sheet: -0.04 (0.18), residues: 772 loop : 1.38 (0.23), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 509 HIS 0.005 0.001 HIS E 79 PHE 0.016 0.002 PHE B 131 TYR 0.020 0.001 TYR F 20 ARG 0.013 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 930) hydrogen bonds : angle 4.76708 ( 2691) covalent geometry : bond 0.00423 (20223) covalent geometry : angle 0.73511 (27351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20716.32 seconds wall clock time: 351 minutes 58.61 seconds (21118.61 seconds total)