Starting phenix.real_space_refine on Tue May 20 05:15:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivs_60934/05_2025/9ivs_60934.cif" } resolution = 2.97 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= 0.008 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 29 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: "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} 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: "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: "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: "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: "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} 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: 11.12, per 1000 atoms: 0.56 Number of scatterers: 19758 At special positions: 0 Unit cell: (113.825, 99.325, 129.05, 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: 4.96 Conformation dependent library (CDL) restraints added in 2.6 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: 83 helices and 30 sheets defined 33.3% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 26 removed outlier: 4.063A pdb=" N ASN A 24 " --> pdb=" O TYR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 32 removed outlier: 4.163A pdb=" N HIS A 31 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.560A pdb=" N ASN A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 103 Processing helix chain 'C' and resid 7 through 26 Processing helix chain 'C' and resid 27 through 32 removed outlier: 4.422A pdb=" N HIS C 31 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'D' and resid 7 through 26 Processing helix chain 'D' and resid 27 through 34 removed outlier: 4.297A 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 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'B' and resid 7 through 23 Processing helix chain 'B' and resid 26 through 32 removed outlier: 4.400A 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 487 Processing helix chain 'L' and resid 499 through 507 Processing helix chain 'I' and resid 481 through 488 Processing helix chain 'I' and resid 499 through 508 removed outlier: 3.600A pdb=" N ASP I 503 " --> pdb=" O GLY I 499 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU I 504 " --> pdb=" O GLU I 500 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR I 505 " --> pdb=" O VAL I 501 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP I 508 " --> pdb=" O LEU I 504 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 26 Processing helix chain 'P' and resid 27 through 32 removed outlier: 4.222A pdb=" N HIS P 31 " --> pdb=" O ASP P 28 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG P 32 " --> pdb=" O MET P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 69 Processing helix chain 'P' and resid 134 through 138 Processing helix chain 'N' and resid 7 through 26 Processing helix chain 'N' and resid 27 through 32 removed outlier: 4.154A pdb=" N HIS N 31 " --> pdb=" O ASP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 68 Processing helix chain 'N' and resid 86 through 88 No H-bonds generated for 'chain 'N' and resid 86 through 88' Processing helix chain 'N' and resid 135 through 137 No H-bonds generated for 'chain 'N' and resid 135 through 137' Processing helix chain 'M' and resid 7 through 26 Processing helix chain 'M' and resid 27 through 34 removed outlier: 4.118A pdb=" N HIS M 31 " --> pdb=" O ASP M 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG M 32 " --> pdb=" O MET M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 69 Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'O' and resid 7 through 26 Processing helix chain 'O' and resid 27 through 32 removed outlier: 4.201A pdb=" N HIS O 31 " --> pdb=" O ASP O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 68 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 Processing helix chain 'V' and resid 499 through 506 Processing helix chain 'U' and resid 481 through 488 Processing helix chain 'U' and resid 499 through 506 removed outlier: 4.048A pdb=" N ASP U 503 " --> pdb=" O GLY U 499 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU U 504 " --> pdb=" O GLU U 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 26 removed outlier: 4.081A pdb=" N ASN T 24 " --> pdb=" O TYR T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 27 through 32 removed outlier: 4.262A pdb=" N HIS T 31 " --> pdb=" O ASP T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 69 removed outlier: 3.711A pdb=" N ASN T 69 " --> pdb=" O VAL T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 103 Processing helix chain 'R' and resid 7 through 26 removed outlier: 3.741A pdb=" N ASN R 24 " --> pdb=" O TYR R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 32 removed outlier: 3.581A pdb=" N HIS R 31 " --> pdb=" O ASP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 68 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 Processing helix chain 'Q' and resid 27 through 34 removed outlier: 4.007A 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 134 through 138 Processing helix chain 'S' and resid 7 through 23 Processing helix chain 'S' and resid 26 through 32 removed outlier: 4.508A pdb=" N HIS S 31 " --> pdb=" O ASP S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 69 Processing helix chain 'S' and resid 134 through 138 Processing helix chain 'X' and resid 481 through 487 Processing helix chain 'X' and resid 499 through 506 Processing helix chain 'W' and resid 481 through 488 Processing helix chain 'W' and resid 499 through 506 removed outlier: 3.603A pdb=" N ASP W 503 " --> pdb=" O GLY W 499 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU W 504 " --> pdb=" O GLU W 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 4.158A pdb=" N ASN E 24 " --> pdb=" O TYR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 removed outlier: 4.114A pdb=" N HIS E 31 " --> pdb=" O ASP E 28 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 32 " --> pdb=" O MET E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 69 Processing helix chain 'G' and resid 7 through 26 Processing helix chain 'G' and resid 27 through 32 removed outlier: 4.188A pdb=" N HIS G 31 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 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 34 removed outlier: 4.228A pdb=" N HIS H 31 " --> pdb=" O ASP H 28 " (cutoff:3.500A) removed outlier: 3.500A 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 25 Processing helix chain 'F' and resid 26 through 32 removed outlier: 4.288A pdb=" N HIS F 31 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 69 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 481 through 488 removed outlier: 3.928A pdb=" N SER J 488 " --> pdb=" O GLU J 484 " (cutoff:3.500A) Processing helix chain 'J' and resid 499 through 507 removed outlier: 3.846A pdb=" N SER J 507 " --> pdb=" O ASP J 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 488 Processing helix chain 'K' and resid 502 through 506 removed outlier: 3.677A pdb=" N ASP K 506 " --> pdb=" O ASP K 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 removed outlier: 10.840A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS A 127 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL A 126 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA A 115 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 97 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ILE A 77 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N SER A 99 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR A 75 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56 removed outlier: 10.840A pdb=" N GLY A 35 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N TYR A 125 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N ASN A 37 " --> pdb=" O TYR A 125 " (cutoff:3.500A) removed outlier: 6.642A 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: 6.391A pdb=" N GLY C 35 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS C 127 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN C 37 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ASP C 129 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER C 39 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE C 131 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL C 41 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR C 133 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 113 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP C 129 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 111 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C 131 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET C 109 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR C 133 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ARG C 107 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 97 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ILE C 77 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER C 99 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 5.271A 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: 6.391A pdb=" N GLY C 35 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N HIS C 127 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN C 37 " --> pdb=" O HIS C 127 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ASP C 129 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER C 39 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE C 131 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL C 41 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR C 133 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 124 " --> pdb=" O THR I 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 55 through 56 removed outlier: 6.784A pdb=" N SER D 39 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE D 131 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 41 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR D 133 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL D 126 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA D 115 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY D 96 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 97 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE D 77 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER D 99 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N THR D 75 " --> pdb=" O SER D 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 55 through 56 removed outlier: 6.784A pdb=" N SER D 39 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N PHE D 131 " --> pdb=" O SER D 39 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL D 41 " --> pdb=" O PHE D 131 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR D 133 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 124 " --> pdb=" O THR J 474 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 56 removed outlier: 11.108A pdb=" N GLY B 35 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N TYR B 125 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ASN B 37 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS B 127 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL B 126 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 115 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 91 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 82 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN B 93 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL B 80 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 6.570A 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: 11.108A pdb=" N GLY B 35 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 9.748A pdb=" N TYR B 125 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ASN B 37 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N HIS B 127 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 124 " --> pdb=" O THR I 474 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 474 through 475 removed outlier: 7.347A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 474 through 475 removed outlier: 7.347A pdb=" N THR L 474 " --> pdb=" O PHE H 124 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N VAL H 126 " --> pdb=" O THR L 474 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL H 126 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA H 115 " --> pdb=" O VAL H 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY H 96 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU H 97 " --> pdb=" O ILE H 77 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE H 77 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER H 99 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.436A 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: 10.549A pdb=" N GLY P 35 " --> pdb=" O LYS P 123 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR P 125 " --> pdb=" O GLY P 35 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ASN P 37 " --> pdb=" O TYR P 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS P 127 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL P 113 " --> pdb=" O HIS P 127 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP P 129 " --> pdb=" O THR P 111 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR P 111 " --> pdb=" O ASP P 129 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE P 131 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET P 109 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR P 133 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ARG P 107 " --> pdb=" O TYR P 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY P 89 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA P 84 " --> pdb=" O GLY P 89 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL P 91 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA P 82 " --> pdb=" O VAL P 91 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN P 93 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL P 80 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET P 95 " --> pdb=" O ARG P 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 55 through 56 removed outlier: 10.549A pdb=" N GLY P 35 " --> pdb=" O LYS P 123 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N TYR P 125 " --> pdb=" O GLY P 35 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N ASN P 37 " --> pdb=" O TYR P 125 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS P 127 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE P 124 " --> pdb=" O THR V 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 34 through 42 removed outlier: 6.451A pdb=" N GLY N 35 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS N 127 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN N 37 " --> pdb=" O HIS N 127 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP N 129 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER N 39 " --> pdb=" O ASP N 129 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE N 131 " --> pdb=" O SER N 39 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL N 41 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N TYR N 133 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL N 113 " --> pdb=" O HIS N 127 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP N 129 " --> pdb=" O THR N 111 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR N 111 " --> pdb=" O ASP N 129 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE N 131 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET N 109 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR N 133 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG N 107 " --> pdb=" O TYR N 133 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL N 91 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA N 82 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN N 93 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL N 80 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.439A 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: 6.451A pdb=" N GLY N 35 " --> pdb=" O TYR N 125 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS N 127 " --> pdb=" O GLY N 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN N 37 " --> pdb=" O HIS N 127 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP N 129 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER N 39 " --> pdb=" O ASP N 129 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE N 131 " --> pdb=" O SER N 39 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL N 41 " --> pdb=" O PHE N 131 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N TYR N 133 " --> pdb=" O VAL N 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 55 through 56 removed outlier: 5.619A pdb=" N VAL M 126 " --> pdb=" O ALA M 115 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA M 115 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY M 96 " --> pdb=" O PHE M 108 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU M 97 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE M 77 " --> pdb=" O LEU M 97 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N SER M 99 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 5.479A 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: 3.622A pdb=" N PHE M 124 " --> pdb=" O THR X 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'O' and resid 55 through 56 removed outlier: 11.399A pdb=" N GLY O 35 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N TYR O 125 " --> pdb=" O GLY O 35 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN O 37 " --> pdb=" O TYR O 125 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS O 127 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL O 126 " --> pdb=" O ALA O 115 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA O 115 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL O 91 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA O 82 " --> pdb=" O VAL O 91 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN O 93 " --> pdb=" O VAL O 80 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL O 80 " --> pdb=" O GLN O 93 " (cutoff:3.500A) removed outlier: 6.576A 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: 11.399A pdb=" N GLY O 35 " --> pdb=" O LYS O 123 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N TYR O 125 " --> pdb=" O GLY O 35 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N ASN O 37 " --> pdb=" O TYR O 125 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N HIS O 127 " --> pdb=" O ASN O 37 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 55 through 56 removed outlier: 10.616A pdb=" N GLY T 35 " --> pdb=" O LYS T 123 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N TYR T 125 " --> pdb=" O GLY T 35 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N ASN T 37 " --> pdb=" O TYR T 125 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS T 127 " --> pdb=" O ASN T 37 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL T 113 " --> pdb=" O HIS T 127 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP T 129 " --> pdb=" O THR T 111 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR T 111 " --> pdb=" O ASP T 129 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE T 131 " --> pdb=" O MET T 109 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N MET T 109 " --> pdb=" O PHE T 131 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TYR T 133 " --> pdb=" O ARG T 107 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ARG T 107 " --> pdb=" O TYR T 133 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU T 97 " --> pdb=" O ILE T 77 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ILE T 77 " --> pdb=" O LEU T 97 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER T 99 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR T 75 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 55 through 56 removed outlier: 10.616A pdb=" N GLY T 35 " --> pdb=" O LYS T 123 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N TYR T 125 " --> pdb=" O GLY T 35 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N ASN T 37 " --> pdb=" O TYR T 125 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS T 127 " --> pdb=" O ASN T 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 55 through 56 removed outlier: 6.430A pdb=" N GLY R 35 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS R 127 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN R 37 " --> pdb=" O HIS R 127 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP R 129 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER R 39 " --> pdb=" O ASP R 129 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE R 131 " --> pdb=" O SER R 39 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL R 41 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR R 133 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL R 126 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA R 115 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL R 91 " --> pdb=" O ALA R 82 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA R 82 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN R 93 " --> pdb=" O VAL R 80 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL R 80 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET R 95 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 55 through 56 removed outlier: 6.430A pdb=" N GLY R 35 " --> pdb=" O TYR R 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N HIS R 127 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN R 37 " --> pdb=" O HIS R 127 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP R 129 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER R 39 " --> pdb=" O ASP R 129 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE R 131 " --> pdb=" O SER R 39 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL R 41 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TYR R 133 " --> pdb=" O VAL R 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 55 through 56 removed outlier: 5.607A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA Q 115 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ILE Q 77 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER Q 99 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR Q 75 " --> pdb=" O SER Q 99 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 55 through 56 removed outlier: 10.718A pdb=" N GLY S 35 " --> pdb=" O LYS S 123 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TYR S 125 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASN S 37 " --> pdb=" O TYR S 125 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS S 127 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL S 126 " --> pdb=" O ALA S 115 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA S 115 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LEU S 97 " --> pdb=" O ILE S 77 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE S 77 " --> pdb=" O LEU S 97 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N SER S 99 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N THR S 75 " --> pdb=" O SER S 99 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 55 through 56 removed outlier: 10.718A pdb=" N GLY S 35 " --> pdb=" O LYS S 123 " (cutoff:3.500A) removed outlier: 9.043A pdb=" N TYR S 125 " --> pdb=" O GLY S 35 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ASN S 37 " --> pdb=" O TYR S 125 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS S 127 " --> pdb=" O ASN S 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 55 through 56 removed outlier: 3.525A pdb=" N VAL E 55 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL E 113 " --> pdb=" O HIS E 127 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP E 129 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR E 111 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE E 131 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N MET E 109 " --> pdb=" O PHE E 131 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR E 133 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ARG E 107 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU E 97 " --> pdb=" O ILE E 77 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE E 77 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER E 99 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N THR E 75 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 55 through 56 removed outlier: 6.561A pdb=" N GLY G 35 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS G 127 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN G 37 " --> pdb=" O HIS G 127 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP G 129 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER G 39 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE G 131 " --> pdb=" O SER G 39 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL G 41 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR G 133 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 113 " --> pdb=" O HIS G 127 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP G 129 " --> pdb=" O THR G 111 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR G 111 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE G 131 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET G 109 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TYR G 133 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG G 107 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL G 91 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA G 82 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN G 93 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL G 80 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET G 95 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 55 through 56 removed outlier: 6.561A pdb=" N GLY G 35 " --> pdb=" O TYR G 125 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS G 127 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN G 37 " --> pdb=" O HIS G 127 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP G 129 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER G 39 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE G 131 " --> pdb=" O SER G 39 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL G 41 " --> pdb=" O PHE G 131 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N TYR G 133 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 55 through 56 removed outlier: 11.297A pdb=" N GLY F 35 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N TYR F 125 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ASN F 37 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS F 127 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N VAL F 126 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA F 115 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL F 91 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA F 82 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN F 93 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 80 " --> pdb=" O GLN F 93 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 95 " --> pdb=" O ARG F 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 55 through 56 removed outlier: 11.297A pdb=" N GLY F 35 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N TYR F 125 " --> pdb=" O GLY F 35 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N ASN F 37 " --> pdb=" O TYR F 125 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N HIS F 127 " --> pdb=" O ASN F 37 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2490 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: 6.23 Time building geometry restraints manager: 5.76 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: 5612 1.33 - 1.46: 4590 1.46 - 1.58: 9860 1.58 - 1.70: 0 1.70 - 1.83: 161 Bond restraints: 20223 Sorted by residual: bond pdb=" N LYS A 50 " pdb=" CA LYS A 50 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.25e+01 bond pdb=" N VAL K 501 " pdb=" CA VAL K 501 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N GLY O 35 " pdb=" CA GLY O 35 " ideal model delta sigma weight residual 1.445 1.477 -0.032 9.90e-03 1.02e+04 1.07e+01 bond pdb=" N VAL A 120 " pdb=" CA VAL A 120 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.07e-02 8.73e+03 1.07e+01 bond pdb=" N GLN M 68 " pdb=" CA GLN M 68 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.50e+00 ... (remaining 20218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 26392 2.46 - 4.92: 858 4.92 - 7.39: 79 7.39 - 9.85: 17 9.85 - 12.31: 5 Bond angle restraints: 27351 Sorted by residual: angle pdb=" N ASP W 495 " pdb=" CA ASP W 495 " pdb=" C ASP W 495 " ideal model delta sigma weight residual 114.12 106.83 7.29 1.39e+00 5.18e-01 2.75e+01 angle pdb=" CA PHE D 138 " pdb=" CB PHE D 138 " pdb=" CG PHE D 138 " ideal model delta sigma weight residual 113.80 118.48 -4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" N SER X 485 " pdb=" CA SER X 485 " pdb=" C SER X 485 " ideal model delta sigma weight residual 112.23 106.48 5.75 1.26e+00 6.30e-01 2.08e+01 angle pdb=" CA ASP U 502 " pdb=" C ASP U 502 " pdb=" O ASP U 502 " ideal model delta sigma weight residual 120.90 116.05 4.85 1.07e+00 8.73e-01 2.06e+01 angle pdb=" N HIS R 62 " pdb=" CA HIS R 62 " pdb=" C HIS R 62 " ideal model delta sigma weight residual 111.07 106.30 4.77 1.07e+00 8.73e-01 1.99e+01 ... (remaining 27346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 10269 17.66 - 35.32: 1322 35.32 - 52.98: 298 52.98 - 70.64: 42 70.64 - 88.30: 22 Dihedral angle restraints: 11953 sinusoidal: 4833 harmonic: 7120 Sorted by residual: dihedral pdb=" C THR U 474 " pdb=" N THR U 474 " pdb=" CA THR U 474 " pdb=" CB THR U 474 " ideal model delta harmonic sigma weight residual -122.00 -133.32 11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" C THR D 85 " pdb=" N THR D 85 " pdb=" CA THR D 85 " pdb=" CB THR D 85 " ideal model delta harmonic sigma weight residual -122.00 -131.96 9.96 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" N THR W 492 " pdb=" C THR W 492 " pdb=" CA THR W 492 " pdb=" CB THR W 492 " ideal model delta harmonic sigma weight residual 123.40 113.56 9.84 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 11950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2373 0.072 - 0.143: 436 0.143 - 0.215: 76 0.215 - 0.287: 15 0.287 - 0.358: 5 Chirality restraints: 2905 Sorted by residual: chirality pdb=" CA VAL P 94 " pdb=" N VAL P 94 " pdb=" C VAL P 94 " pdb=" CB VAL P 94 " both_signs ideal model delta sigma weight residual False 2.44 2.80 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA THR W 492 " pdb=" N THR W 492 " pdb=" C THR W 492 " pdb=" CB THR W 492 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA VAL T 94 " pdb=" N VAL T 94 " pdb=" C VAL T 94 " pdb=" CB VAL T 94 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2902 not shown) Planarity restraints: 3638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 71 " -0.021 2.00e-02 2.50e+03 4.35e-02 1.90e+01 pdb=" C THR A 71 " 0.075 2.00e-02 2.50e+03 pdb=" O THR A 71 " -0.029 2.00e-02 2.50e+03 pdb=" N ASN A 72 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 26 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO G 27 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 27 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 27 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP U 503 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.48e+00 pdb=" CG ASP U 503 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP U 503 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP U 503 " -0.017 2.00e-02 2.50e+03 ... (remaining 3635 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 815 2.71 - 3.25: 20054 3.25 - 3.80: 32863 3.80 - 4.35: 41353 4.35 - 4.90: 70360 Nonbonded interactions: 165445 Sorted by model distance: nonbonded pdb=" O ASN N 69 " pdb=" OD1 ASN N 69 " model vdw 2.156 3.040 nonbonded pdb=" N GLN C 103 " pdb=" OE1 GLN C 103 " model vdw 2.180 3.120 nonbonded pdb=" O GLY V 476 " pdb=" CE LYS Q 123 " model vdw 2.195 3.440 nonbonded pdb=" OH TYR C 34 " pdb=" OD2 ASP C 129 " model vdw 2.209 3.040 nonbonded pdb=" OH TYR N 20 " pdb=" OE1 GLN N 110 " model vdw 2.218 3.040 ... (remaining 165440 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: 1.840 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: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 43.860 Find NCS groups from input model: 1.030 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:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.080 20223 Z= 0.397 Angle : 0.955 12.311 27351 Z= 0.595 Chirality : 0.060 0.358 2905 Planarity : 0.005 0.082 3638 Dihedral : 16.305 88.297 7383 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 3.01 % Allowed : 29.53 % Favored : 67.45 % Cbeta Deviations : 0.09 % 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: 0.63 (0.18), residues: 2415 helix: 1.50 (0.20), residues: 620 sheet: -0.20 (0.18), residues: 770 loop : 0.44 (0.23), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP U 509 HIS 0.013 0.001 HIS O 79 PHE 0.032 0.002 PHE K 493 TYR 0.025 0.002 TYR S 125 ARG 0.010 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.11894 ( 892) hydrogen bonds : angle 6.08173 ( 2490) covalent geometry : bond 0.00647 (20223) covalent geometry : angle 0.95535 (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 660 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 595 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 63 ARG cc_start: 0.9359 (ptm160) cc_final: 0.9102 (ptm-80) REVERT: C 81 ASP cc_start: 0.8293 (t0) cc_final: 0.7593 (t0) REVERT: C 101 ASN cc_start: 0.8803 (m-40) cc_final: 0.8422 (m-40) REVERT: C 109 MET cc_start: 0.8142 (mtp) cc_final: 0.7276 (ttm) REVERT: D 29 MET cc_start: 0.9208 (mtm) cc_final: 0.8919 (mtm) REVERT: D 32 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8809 (mmm-85) REVERT: D 37 ASN cc_start: 0.9291 (t0) cc_final: 0.8763 (p0) REVERT: D 78 ARG cc_start: 0.8971 (tpm170) cc_final: 0.8517 (ttm-80) REVERT: D 81 ASP cc_start: 0.8486 (m-30) cc_final: 0.8128 (m-30) REVERT: B 59 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8614 (mmmt) REVERT: B 63 ARG cc_start: 0.9238 (tmm-80) cc_final: 0.9003 (tmm-80) REVERT: L 502 ASP cc_start: 0.8233 (m-30) cc_final: 0.7346 (p0) REVERT: P 59 LYS cc_start: 0.9228 (ttpt) cc_final: 0.9021 (mmtt) REVERT: N 3 MET cc_start: 0.6918 (tpp) cc_final: 0.6634 (tpp) REVERT: N 29 MET cc_start: 0.8585 (tpp) cc_final: 0.8209 (tpt) REVERT: N 62 HIS cc_start: 0.8816 (t70) cc_final: 0.8354 (t-90) REVERT: M 18 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8494 (mm-40) REVERT: M 32 ARG cc_start: 0.9039 (mmm-85) cc_final: 0.8268 (mmm-85) REVERT: M 59 LYS cc_start: 0.9141 (tptt) cc_final: 0.8864 (tptp) REVERT: U 496 PHE cc_start: 0.8813 (m-80) cc_final: 0.8519 (m-10) REVERT: R 29 MET cc_start: 0.8687 (mmm) cc_final: 0.8168 (mmm) REVERT: Q 32 ARG cc_start: 0.9068 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: X 500 GLU cc_start: 0.8748 (tt0) cc_final: 0.7906 (tt0) REVERT: W 479 ASN cc_start: 0.8671 (t0) cc_final: 0.8329 (t0) REVERT: W 480 ASP cc_start: 0.8976 (p0) cc_final: 0.8664 (p0) REVERT: W 489 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8401 (mm-30) REVERT: E 59 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8865 (mmpt) REVERT: J 506 ASP cc_start: 0.7734 (p0) cc_final: 0.7463 (p0) REVERT: K 500 GLU cc_start: 0.9140 (tt0) cc_final: 0.8597 (tm-30) outliers start: 65 outliers final: 42 residues processed: 639 average time/residue: 1.1424 time to fit residues: 831.1105 Evaluate side-chains 552 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 509 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain P residue 87 ASN Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 29 MET Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain O residue 86 LEU 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 U residue 491 LEU Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 109 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 GLU Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 495 ASP Chi-restraints excluded: chain K 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: 5.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 210 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN A 128 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN N 37 ASN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS T 103 GLN T 128 ASN R 24 ASN ** Q 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 ASN Q 74 HIS S 37 ASN S 48 ASN S 128 ASN E 103 GLN G 58 GLN G 128 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092682 restraints weight = 61567.490| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 5.20 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20223 Z= 0.142 Angle : 0.653 10.987 27351 Z= 0.333 Chirality : 0.044 0.179 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.855 73.590 2767 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.68 % Favored : 95.27 % Rotamer: Outliers : 5.66 % Allowed : 28.37 % Favored : 65.97 % 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: 1.05 (0.18), residues: 2415 helix: 1.84 (0.20), residues: 620 sheet: 0.12 (0.19), residues: 668 loop : 0.58 (0.21), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 509 HIS 0.008 0.001 HIS O 79 PHE 0.018 0.002 PHE A 15 TYR 0.018 0.002 TYR N 20 ARG 0.006 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 892) hydrogen bonds : angle 5.05625 ( 2490) covalent geometry : bond 0.00329 (20223) covalent geometry : angle 0.65328 (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 686 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 564 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7331 (t0) cc_final: 0.7124 (t0) REVERT: A 88 ASP cc_start: 0.8173 (t0) cc_final: 0.7903 (t0) REVERT: C 63 ARG cc_start: 0.9345 (ptm160) cc_final: 0.9023 (ptm-80) REVERT: C 66 MET cc_start: 0.9135 (mmm) cc_final: 0.8891 (mmm) REVERT: C 81 ASP cc_start: 0.8309 (t0) cc_final: 0.7525 (t0) REVERT: D 9 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8897 (tm) REVERT: D 32 ARG cc_start: 0.8958 (mtp85) cc_final: 0.8743 (mmm-85) REVERT: D 78 ARG cc_start: 0.8738 (tpm170) cc_final: 0.8013 (tpp-160) REVERT: D 81 ASP cc_start: 0.8374 (m-30) cc_final: 0.8110 (m-30) REVERT: B 29 MET cc_start: 0.9030 (mpp) cc_final: 0.8765 (mpp) REVERT: B 59 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8594 (mmmt) REVERT: B 63 ARG cc_start: 0.9140 (tmm-80) cc_final: 0.8905 (tmm-80) REVERT: L 482 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: L 502 ASP cc_start: 0.7981 (m-30) cc_final: 0.7747 (m-30) REVERT: L 503 ASP cc_start: 0.8334 (m-30) cc_final: 0.7955 (m-30) REVERT: I 495 ASP cc_start: 0.8381 (t0) cc_final: 0.8155 (t0) REVERT: I 496 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: P 59 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8930 (mptt) REVERT: P 88 ASP cc_start: 0.7940 (t0) cc_final: 0.7725 (t0) REVERT: P 109 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8417 (ptp) REVERT: N 1 MET cc_start: 0.7377 (tpp) cc_final: 0.7037 (tpp) REVERT: N 14 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6968 (tm-30) REVERT: N 29 MET cc_start: 0.8543 (tpp) cc_final: 0.8231 (tpt) REVERT: N 62 HIS cc_start: 0.8632 (t70) cc_final: 0.8253 (t-90) REVERT: N 107 ARG cc_start: 0.7354 (mmt90) cc_final: 0.7016 (mmt90) REVERT: N 117 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8139 (tm-30) REVERT: M 25 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8643 (mm-40) REVERT: M 32 ARG cc_start: 0.9000 (mmm-85) cc_final: 0.8619 (mmm-85) REVERT: M 59 LYS cc_start: 0.9020 (tptt) cc_final: 0.8794 (tptp) REVERT: M 66 MET cc_start: 0.8984 (mmm) cc_final: 0.8512 (mmm) REVERT: M 103 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: M 123 LYS cc_start: 0.8445 (tppt) cc_final: 0.8102 (tppt) REVERT: O 36 LYS cc_start: 0.9096 (pmmt) cc_final: 0.8886 (pptt) REVERT: O 60 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8346 (mm-30) REVERT: O 63 ARG cc_start: 0.9152 (ttt-90) cc_final: 0.8474 (ttp80) REVERT: O 103 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: O 123 LYS cc_start: 0.8926 (tppp) cc_final: 0.8686 (tptp) REVERT: U 491 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7935 (tm) REVERT: U 493 PHE cc_start: 0.8416 (m-80) cc_final: 0.8172 (m-80) REVERT: U 496 PHE cc_start: 0.8642 (m-80) cc_final: 0.8297 (m-10) REVERT: T 76 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7995 (tptp) REVERT: T 88 ASP cc_start: 0.8044 (t0) cc_final: 0.7833 (t0) REVERT: R 29 MET cc_start: 0.8601 (mmm) cc_final: 0.8203 (mmm) REVERT: R 62 HIS cc_start: 0.8638 (t-90) cc_final: 0.8392 (t70) REVERT: R 63 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8434 (ttp80) REVERT: R 66 MET cc_start: 0.9044 (mmm) cc_final: 0.8834 (mmm) REVERT: Q 14 GLU cc_start: 0.9240 (tp30) cc_final: 0.9038 (tp30) REVERT: Q 32 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8587 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8539 (pp30) cc_final: 0.7649 (pp30) REVERT: Q 123 LYS cc_start: 0.8549 (tptt) cc_final: 0.8292 (tptt) REVERT: Q 134 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7838 (tm-30) REVERT: S 81 ASP cc_start: 0.8093 (t0) cc_final: 0.7864 (t0) REVERT: W 479 ASN cc_start: 0.8599 (t0) cc_final: 0.8296 (t0) REVERT: W 480 ASP cc_start: 0.8822 (p0) cc_final: 0.8575 (p0) REVERT: W 489 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8416 (mm-30) REVERT: E 59 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8721 (mmmt) REVERT: G 3 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6951 (tpp) REVERT: G 68 GLN cc_start: 0.7824 (mt0) cc_final: 0.7528 (mp10) REVERT: G 81 ASP cc_start: 0.8305 (t0) cc_final: 0.7875 (t0) REVERT: G 109 MET cc_start: 0.7165 (mtp) cc_final: 0.6800 (mtp) REVERT: G 134 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: H 17 ARG cc_start: 0.8874 (ppp80) cc_final: 0.8489 (ptm-80) REVERT: H 32 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8796 (mmm-85) REVERT: H 60 GLU cc_start: 0.8878 (mp0) cc_final: 0.8553 (mp0) REVERT: H 68 GLN cc_start: 0.7363 (tm-30) cc_final: 0.7126 (tm-30) REVERT: H 81 ASP cc_start: 0.8393 (m-30) cc_final: 0.7791 (m-30) REVERT: F 29 MET cc_start: 0.9144 (mpp) cc_final: 0.8938 (mpp) REVERT: K 495 ASP cc_start: 0.8877 (t0) cc_final: 0.8674 (t0) REVERT: K 496 PHE cc_start: 0.8450 (m-80) cc_final: 0.7923 (m-80) REVERT: K 500 GLU cc_start: 0.9129 (tt0) cc_final: 0.8843 (tp30) outliers start: 122 outliers final: 52 residues processed: 643 average time/residue: 1.1215 time to fit residues: 823.5695 Evaluate side-chains 594 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 531 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 482 GLU Chi-restraints excluded: chain L residue 492 THR Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 487 SER Chi-restraints excluded: chain I residue 496 PHE Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain U residue 491 LEU Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 95 MET Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 3 MET Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain J residue 473 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 163 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 62 optimal weight: 50.0000 chunk 210 optimal weight: 4.9990 chunk 104 optimal weight: 0.0020 chunk 162 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.0670 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN P 68 GLN N 24 ASN N 37 ASN ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 ASN T 42 HIS T 79 HIS T 103 GLN Q 69 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** 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 = 0.3936 r_free = 0.3936 target = 0.119046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.094005 restraints weight = 70795.904| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 5.53 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20223 Z= 0.119 Angle : 0.634 8.290 27351 Z= 0.318 Chirality : 0.044 0.192 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.135 68.414 2730 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 6.03 % Allowed : 28.84 % Favored : 65.14 % 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: 1.19 (0.18), residues: 2415 helix: 1.92 (0.20), residues: 624 sheet: 0.16 (0.18), residues: 708 loop : 0.75 (0.22), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.014 0.001 HIS B 79 PHE 0.019 0.001 PHE D 15 TYR 0.023 0.001 TYR G 40 ARG 0.007 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03236 ( 892) hydrogen bonds : angle 4.80403 ( 2490) covalent geometry : bond 0.00270 (20223) covalent geometry : angle 0.63408 (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 711 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 581 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7438 (t0) cc_final: 0.7172 (t0) REVERT: A 88 ASP cc_start: 0.8256 (t0) cc_final: 0.7961 (t0) REVERT: A 117 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8595 (mm-30) REVERT: C 63 ARG cc_start: 0.9332 (ptm160) cc_final: 0.9009 (ptm-80) REVERT: C 66 MET cc_start: 0.9233 (mmm) cc_final: 0.8961 (mmm) REVERT: C 81 ASP cc_start: 0.8211 (t0) cc_final: 0.7440 (t0) REVERT: D 28 ASP cc_start: 0.8324 (p0) cc_final: 0.8078 (p0) REVERT: D 29 MET cc_start: 0.9036 (mtm) cc_final: 0.8718 (pmm) REVERT: D 32 ARG cc_start: 0.8948 (mtp85) cc_final: 0.8648 (mmm-85) REVERT: D 66 MET cc_start: 0.9038 (mmp) cc_final: 0.8826 (mmm) REVERT: D 78 ARG cc_start: 0.8690 (tpm170) cc_final: 0.7985 (tpp-160) REVERT: D 81 ASP cc_start: 0.8461 (m-30) cc_final: 0.8256 (m-30) REVERT: D 90 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7068 (p) REVERT: D 95 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6393 (mtt) REVERT: B 59 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8564 (mmmt) REVERT: B 63 ARG cc_start: 0.9152 (tmm-80) cc_final: 0.8887 (tmm-80) REVERT: B 136 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8381 (mp0) REVERT: I 495 ASP cc_start: 0.8466 (t0) cc_final: 0.8183 (t0) REVERT: P 59 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8909 (mmtt) REVERT: P 123 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8152 (tptp) REVERT: N 3 MET cc_start: 0.6660 (tpp) cc_final: 0.6350 (tpp) REVERT: N 14 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7061 (tm-30) REVERT: N 29 MET cc_start: 0.8534 (tpp) cc_final: 0.8036 (mmm) REVERT: N 32 ARG cc_start: 0.8569 (mtp180) cc_final: 0.7890 (ttp80) REVERT: N 62 HIS cc_start: 0.8629 (t70) cc_final: 0.8237 (t-90) REVERT: N 107 ARG cc_start: 0.7450 (mmt90) cc_final: 0.7134 (mmt90) REVERT: N 117 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8134 (tm-30) REVERT: M 25 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8629 (mm-40) REVERT: M 32 ARG cc_start: 0.8962 (mmm-85) cc_final: 0.8511 (mmm-85) REVERT: M 66 MET cc_start: 0.9033 (mmm) cc_final: 0.8599 (mmm) REVERT: M 123 LYS cc_start: 0.8572 (tppt) cc_final: 0.8325 (tppt) REVERT: O 60 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8385 (mm-30) REVERT: O 63 ARG cc_start: 0.9158 (ttt-90) cc_final: 0.8459 (ttp80) REVERT: O 103 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: O 123 LYS cc_start: 0.8952 (tppp) cc_final: 0.8703 (tptp) REVERT: U 479 ASN cc_start: 0.8480 (t0) cc_final: 0.8096 (t0) REVERT: U 491 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8213 (tm) REVERT: U 495 ASP cc_start: 0.9000 (p0) cc_final: 0.8551 (p0) REVERT: U 500 GLU cc_start: 0.8761 (tt0) cc_final: 0.8387 (tt0) REVERT: T 76 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7973 (tptp) REVERT: T 88 ASP cc_start: 0.8051 (t0) cc_final: 0.7830 (t0) REVERT: R 29 MET cc_start: 0.8676 (mmm) cc_final: 0.8246 (mmm) REVERT: R 62 HIS cc_start: 0.8650 (t-90) cc_final: 0.8228 (t70) REVERT: R 66 MET cc_start: 0.9102 (mmm) cc_final: 0.8786 (mmm) REVERT: Q 14 GLU cc_start: 0.9263 (tp30) cc_final: 0.8960 (tp30) REVERT: Q 32 ARG cc_start: 0.8906 (mmm-85) cc_final: 0.8704 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8547 (pp30) cc_final: 0.7769 (pp30) REVERT: Q 134 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7768 (tm-30) REVERT: Q 136 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: S 81 ASP cc_start: 0.8152 (t0) cc_final: 0.7783 (t0) REVERT: S 101 ASN cc_start: 0.9066 (t0) cc_final: 0.8745 (t0) REVERT: W 479 ASN cc_start: 0.8630 (t0) cc_final: 0.8325 (t0) REVERT: W 480 ASP cc_start: 0.8757 (p0) cc_final: 0.8490 (p0) REVERT: W 496 PHE cc_start: 0.8491 (m-80) cc_final: 0.8247 (m-80) REVERT: E 59 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8739 (mmmt) REVERT: G 1 MET cc_start: 0.7408 (tpp) cc_final: 0.6915 (tpp) REVERT: G 3 MET cc_start: 0.7094 (mmm) cc_final: 0.6849 (tpp) REVERT: G 48 ASN cc_start: 0.9162 (t0) cc_final: 0.8847 (p0) REVERT: G 68 GLN cc_start: 0.7714 (mt0) cc_final: 0.7390 (mp10) REVERT: G 109 MET cc_start: 0.7762 (mtp) cc_final: 0.7098 (mtp) REVERT: G 134 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: H 32 ARG cc_start: 0.9049 (mmm-85) cc_final: 0.8848 (mmm-85) REVERT: H 60 GLU cc_start: 0.8965 (mp0) cc_final: 0.8696 (mp0) REVERT: H 63 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8660 (ttp-110) REVERT: H 66 MET cc_start: 0.8831 (mmp) cc_final: 0.8517 (mmm) REVERT: H 68 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7101 (tm-30) REVERT: H 81 ASP cc_start: 0.8483 (m-30) cc_final: 0.7922 (m-30) REVERT: F 39 SER cc_start: 0.9446 (t) cc_final: 0.9157 (p) REVERT: J 482 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: K 495 ASP cc_start: 0.8863 (t0) cc_final: 0.8588 (OUTLIER) REVERT: K 496 PHE cc_start: 0.8560 (m-80) cc_final: 0.7949 (m-80) REVERT: K 500 GLU cc_start: 0.9134 (tt0) cc_final: 0.8848 (tp30) outliers start: 130 outliers final: 50 residues processed: 664 average time/residue: 1.1348 time to fit residues: 857.2609 Evaluate side-chains 591 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 532 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 483 ILE Chi-restraints excluded: chain V residue 486 LEU Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain U residue 491 LEU Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 39 SER Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 482 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 143 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 103 GLN A 128 ASN C 42 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN N 93 GLN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS T 68 GLN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 ASN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 48 ASN ** S 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN G 42 HIS ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.113905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.088492 restraints weight = 70856.212| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 5.50 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3447 r_free = 0.3447 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20223 Z= 0.186 Angle : 0.673 11.534 27351 Z= 0.339 Chirality : 0.045 0.188 2905 Planarity : 0.004 0.049 3638 Dihedral : 5.212 59.620 2719 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.66 % Allowed : 30.55 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.18), residues: 2415 helix: 2.00 (0.20), residues: 616 sheet: 0.02 (0.18), residues: 724 loop : 0.69 (0.22), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP U 509 HIS 0.016 0.001 HIS O 79 PHE 0.023 0.002 PHE D 15 TYR 0.013 0.002 TYR G 19 ARG 0.008 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 892) hydrogen bonds : angle 4.85904 ( 2490) covalent geometry : bond 0.00432 (20223) covalent geometry : angle 0.67251 (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 651 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 529 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 HIS cc_start: 0.8068 (t-90) cc_final: 0.7851 (t70) REVERT: A 81 ASP cc_start: 0.7450 (t0) cc_final: 0.7079 (t0) REVERT: A 88 ASP cc_start: 0.8346 (t0) cc_final: 0.8018 (t0) REVERT: A 117 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8647 (mm-30) REVERT: A 132 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7750 (mtp85) REVERT: C 29 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8738 (ttm) REVERT: C 63 ARG cc_start: 0.9376 (ptm160) cc_final: 0.9073 (ptm-80) REVERT: C 66 MET cc_start: 0.9229 (mmm) cc_final: 0.8996 (mmm) REVERT: C 88 ASP cc_start: 0.7590 (t0) cc_final: 0.7335 (t0) REVERT: C 107 ARG cc_start: 0.7363 (mmt90) cc_final: 0.7028 (mmt90) REVERT: D 28 ASP cc_start: 0.8343 (p0) cc_final: 0.8078 (p0) REVERT: D 29 MET cc_start: 0.9053 (mtm) cc_final: 0.8610 (pmm) REVERT: D 68 GLN cc_start: 0.7258 (tm-30) cc_final: 0.7056 (tm-30) REVERT: D 78 ARG cc_start: 0.8635 (tpm170) cc_final: 0.7951 (tpp-160) REVERT: D 81 ASP cc_start: 0.8388 (m-30) cc_final: 0.7989 (m-30) REVERT: D 90 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7061 (p) REVERT: D 93 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8214 (tm-30) REVERT: B 29 MET cc_start: 0.9063 (mpp) cc_final: 0.8824 (mpp) REVERT: B 59 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8629 (mmmt) REVERT: B 63 ARG cc_start: 0.9171 (tmm-80) cc_final: 0.8897 (tmm-80) REVERT: L 482 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7809 (pm20) REVERT: L 486 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8277 (mp) REVERT: L 502 ASP cc_start: 0.7737 (m-30) cc_final: 0.7286 (p0) REVERT: I 484 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8084 (mm-30) REVERT: I 495 ASP cc_start: 0.8550 (t70) cc_final: 0.8243 (t0) REVERT: P 59 LYS cc_start: 0.9139 (ttpt) cc_final: 0.8930 (mmtt) REVERT: P 88 ASP cc_start: 0.8287 (t0) cc_final: 0.7801 (t0) REVERT: P 123 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8189 (tptp) REVERT: N 1 MET cc_start: 0.7216 (tpt) cc_final: 0.6780 (tpp) REVERT: N 3 MET cc_start: 0.7101 (tpp) cc_final: 0.6761 (tpp) REVERT: N 14 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7015 (tm-30) REVERT: N 29 MET cc_start: 0.8640 (tpp) cc_final: 0.7938 (mmm) REVERT: N 32 ARG cc_start: 0.8645 (mtp180) cc_final: 0.7934 (mtp85) REVERT: N 62 HIS cc_start: 0.8635 (t70) cc_final: 0.8277 (t-90) REVERT: N 107 ARG cc_start: 0.7465 (mmt90) cc_final: 0.7031 (mmt90) REVERT: N 117 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8119 (tm-30) REVERT: M 17 ARG cc_start: 0.9032 (ppp80) cc_final: 0.8674 (ptm-80) REVERT: M 25 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8650 (mm-40) REVERT: M 32 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8631 (mmm-85) REVERT: M 59 LYS cc_start: 0.9066 (tptp) cc_final: 0.8851 (tptp) REVERT: M 103 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: O 59 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8540 (mmmt) REVERT: O 60 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8397 (mm-30) REVERT: O 103 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.6902 (mp10) REVERT: O 123 LYS cc_start: 0.8994 (tppp) cc_final: 0.8711 (tptp) REVERT: U 479 ASN cc_start: 0.8550 (t0) cc_final: 0.8171 (t0) REVERT: T 76 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7990 (tptt) REVERT: T 88 ASP cc_start: 0.8243 (t0) cc_final: 0.7991 (t0) REVERT: R 29 MET cc_start: 0.8755 (mmm) cc_final: 0.8369 (mmm) REVERT: R 63 ARG cc_start: 0.9302 (mtp-110) cc_final: 0.8977 (ttm-80) REVERT: R 66 MET cc_start: 0.9120 (mmm) cc_final: 0.8902 (mmm) REVERT: R 107 ARG cc_start: 0.6887 (mmt90) cc_final: 0.6668 (mmt90) REVERT: Q 14 GLU cc_start: 0.9299 (tp30) cc_final: 0.8956 (tp30) REVERT: Q 93 GLN cc_start: 0.8629 (pp30) cc_final: 0.7831 (pp30) REVERT: Q 134 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7973 (tm-30) REVERT: Q 136 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8386 (pp20) REVERT: W 479 ASN cc_start: 0.8640 (t0) cc_final: 0.8354 (t0) REVERT: W 480 ASP cc_start: 0.8817 (p0) cc_final: 0.8568 (p0) REVERT: E 32 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8455 (mtp85) REVERT: E 59 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8691 (mmmt) REVERT: E 88 ASP cc_start: 0.8131 (t0) cc_final: 0.7863 (t0) REVERT: G 25 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8267 (mm-40) REVERT: G 48 ASN cc_start: 0.9230 (t0) cc_final: 0.8884 (p0) REVERT: G 68 GLN cc_start: 0.7701 (mt0) cc_final: 0.7377 (mp10) REVERT: H 17 ARG cc_start: 0.8975 (ppp80) cc_final: 0.8617 (ptm-80) REVERT: H 56 TYR cc_start: 0.9045 (m-80) cc_final: 0.8726 (m-80) REVERT: H 60 GLU cc_start: 0.8988 (mp0) cc_final: 0.8635 (mp0) REVERT: H 68 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7251 (tm-30) REVERT: H 81 ASP cc_start: 0.8571 (m-30) cc_final: 0.8004 (m-30) REVERT: H 106 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7943 (mtp180) REVERT: F 29 MET cc_start: 0.9066 (mpp) cc_final: 0.8813 (mpp) REVERT: F 103 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: F 123 LYS cc_start: 0.8971 (tppp) cc_final: 0.8615 (tptp) REVERT: K 495 ASP cc_start: 0.8942 (t0) cc_final: 0.8624 (t0) REVERT: K 496 PHE cc_start: 0.8857 (m-80) cc_final: 0.8363 (m-80) REVERT: K 500 GLU cc_start: 0.9270 (tt0) cc_final: 0.8779 (tp30) outliers start: 122 outliers final: 58 residues processed: 610 average time/residue: 1.1701 time to fit residues: 811.1169 Evaluate side-chains 584 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 513 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 482 GLU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 487 SER Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain U residue 491 LEU Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 506 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: 4.9990 chunk 19 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 42 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Q 128 ASN S 128 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089240 restraints weight = 49222.493| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 4.58 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20223 Z= 0.178 Angle : 0.674 9.975 27351 Z= 0.339 Chirality : 0.044 0.170 2905 Planarity : 0.004 0.053 3638 Dihedral : 5.093 56.449 2719 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 6.07 % Allowed : 30.13 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.18), residues: 2415 helix: 1.98 (0.20), residues: 620 sheet: -0.05 (0.18), residues: 724 loop : 0.71 (0.22), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.012 0.001 HIS O 79 PHE 0.018 0.002 PHE F 131 TYR 0.025 0.002 TYR C 40 ARG 0.009 0.001 ARG Q 32 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 892) hydrogen bonds : angle 4.88738 ( 2490) covalent geometry : bond 0.00416 (20223) covalent geometry : angle 0.67412 (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 670 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 539 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7507 (t0) cc_final: 0.7099 (t0) REVERT: A 88 ASP cc_start: 0.8391 (t0) cc_final: 0.8039 (t0) REVERT: A 117 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8579 (mm-30) REVERT: A 132 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7347 (mtp85) REVERT: C 63 ARG cc_start: 0.9385 (ptm160) cc_final: 0.9068 (ptm-80) REVERT: C 66 MET cc_start: 0.9222 (mmm) cc_final: 0.8985 (mmm) REVERT: C 88 ASP cc_start: 0.7720 (t0) cc_final: 0.7461 (t0) REVERT: D 17 ARG cc_start: 0.9037 (ppp80) cc_final: 0.8661 (ptm-80) REVERT: D 32 ARG cc_start: 0.8860 (mtm180) cc_final: 0.8284 (mtp180) REVERT: D 68 GLN cc_start: 0.7254 (tm-30) cc_final: 0.7002 (tm-30) REVERT: D 78 ARG cc_start: 0.8652 (tpm170) cc_final: 0.7964 (tpp-160) REVERT: D 81 ASP cc_start: 0.8395 (m-30) cc_final: 0.7938 (m-30) REVERT: D 90 VAL cc_start: 0.7466 (OUTLIER) cc_final: 0.7069 (p) REVERT: D 93 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8106 (tm-30) REVERT: B 59 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8617 (mmmt) REVERT: B 63 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8886 (tmm-80) REVERT: B 109 MET cc_start: 0.8038 (mtt) cc_final: 0.7827 (mtt) REVERT: L 482 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: L 486 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8255 (mp) REVERT: L 502 ASP cc_start: 0.7810 (m-30) cc_final: 0.7378 (p0) REVERT: I 479 ASN cc_start: 0.8795 (t0) cc_final: 0.8505 (t0) REVERT: I 495 ASP cc_start: 0.8581 (t70) cc_final: 0.8251 (t0) REVERT: P 88 ASP cc_start: 0.8308 (t0) cc_final: 0.7889 (t0) REVERT: P 123 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8163 (tptp) REVERT: N 1 MET cc_start: 0.7195 (tpt) cc_final: 0.6604 (tpp) REVERT: N 3 MET cc_start: 0.7181 (tpp) cc_final: 0.6836 (tpp) REVERT: N 14 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7064 (tm-30) REVERT: N 32 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8382 (mmm-85) REVERT: N 62 HIS cc_start: 0.8593 (t70) cc_final: 0.8388 (t-90) REVERT: N 117 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8140 (tm-30) REVERT: M 25 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8603 (mm-40) REVERT: M 32 ARG cc_start: 0.8997 (mmm-85) cc_final: 0.8537 (mmm-85) REVERT: O 59 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8547 (mmmt) REVERT: O 60 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8268 (mm-30) REVERT: O 63 ARG cc_start: 0.9182 (ttt-90) cc_final: 0.8498 (ttp80) REVERT: O 103 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6967 (mp10) REVERT: U 479 ASN cc_start: 0.8584 (t0) cc_final: 0.8182 (t0) REVERT: U 495 ASP cc_start: 0.8936 (p0) cc_final: 0.8450 (p0) REVERT: T 76 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8122 (tptt) REVERT: T 88 ASP cc_start: 0.8302 (t0) cc_final: 0.8015 (t0) REVERT: R 63 ARG cc_start: 0.9287 (mtp-110) cc_final: 0.8940 (ttm-80) REVERT: R 68 GLN cc_start: 0.7782 (mp10) cc_final: 0.7387 (mp10) REVERT: Q 93 GLN cc_start: 0.8619 (pp30) cc_final: 0.7965 (pp30) REVERT: Q 134 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8069 (tm-30) REVERT: W 479 ASN cc_start: 0.8648 (t0) cc_final: 0.8364 (t0) REVERT: W 480 ASP cc_start: 0.8816 (p0) cc_final: 0.8568 (p0) REVERT: W 496 PHE cc_start: 0.8548 (m-80) cc_final: 0.8166 (m-10) REVERT: E 14 GLU cc_start: 0.8608 (tp30) cc_final: 0.8401 (tp30) REVERT: E 59 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8690 (mmmt) REVERT: E 76 LYS cc_start: 0.8166 (tptt) cc_final: 0.7528 (tptp) REVERT: E 88 ASP cc_start: 0.8105 (t0) cc_final: 0.7769 (t0) REVERT: G 25 GLN cc_start: 0.8544 (mm-40) cc_final: 0.8299 (mm-40) REVERT: G 48 ASN cc_start: 0.9238 (t0) cc_final: 0.8913 (p0) REVERT: G 68 GLN cc_start: 0.7660 (mt0) cc_final: 0.7291 (mp10) REVERT: G 81 ASP cc_start: 0.8155 (t0) cc_final: 0.7587 (t0) REVERT: H 17 ARG cc_start: 0.8984 (ppp80) cc_final: 0.8566 (ptm-80) REVERT: H 32 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8717 (mmm-85) REVERT: H 56 TYR cc_start: 0.9028 (m-80) cc_final: 0.8733 (m-80) REVERT: H 60 GLU cc_start: 0.8953 (mp0) cc_final: 0.8611 (mp0) REVERT: H 68 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7333 (tm-30) REVERT: H 81 ASP cc_start: 0.8594 (m-30) cc_final: 0.7988 (m-30) REVERT: H 106 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7976 (mtp180) REVERT: F 103 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: F 123 LYS cc_start: 0.8945 (tppp) cc_final: 0.8561 (tptp) REVERT: J 482 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: K 495 ASP cc_start: 0.8932 (t0) cc_final: 0.8589 (t0) REVERT: K 496 PHE cc_start: 0.8891 (m-80) cc_final: 0.8467 (m-80) REVERT: K 500 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: K 503 ASP cc_start: 0.9404 (p0) cc_final: 0.8720 (OUTLIER) outliers start: 131 outliers final: 69 residues processed: 619 average time/residue: 1.1589 time to fit residues: 815.3561 Evaluate side-chains 595 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 514 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 482 GLU Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 487 SER Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 483 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain U residue 490 LEU Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 103 GLN 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 473 ILE Chi-restraints excluded: chain J residue 482 GLU Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain J residue 506 ASP Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 130 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 128 ASN C 42 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 48 ASN S 68 GLN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS H 42 HIS ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.114842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.090305 restraints weight = 68089.028| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 5.32 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20223 Z= 0.143 Angle : 0.690 12.016 27351 Z= 0.342 Chirality : 0.045 0.165 2905 Planarity : 0.004 0.053 3638 Dihedral : 4.988 57.477 2717 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 5.29 % Allowed : 31.85 % Favored : 62.87 % 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: 1.07 (0.18), residues: 2415 helix: 2.00 (0.20), residues: 616 sheet: -0.10 (0.18), residues: 728 loop : 0.73 (0.22), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.010 0.001 HIS O 79 PHE 0.017 0.002 PHE O 131 TYR 0.022 0.002 TYR C 40 ARG 0.009 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 892) hydrogen bonds : angle 4.83876 ( 2490) covalent geometry : bond 0.00336 (20223) covalent geometry : angle 0.68984 (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 663 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 549 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7508 (t0) cc_final: 0.7083 (t0) REVERT: A 88 ASP cc_start: 0.8454 (t0) cc_final: 0.8102 (t0) REVERT: A 117 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8600 (mm-30) REVERT: A 132 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7436 (mtp85) REVERT: C 63 ARG cc_start: 0.9375 (ptm160) cc_final: 0.9058 (ptm-80) REVERT: C 66 MET cc_start: 0.9219 (mmm) cc_final: 0.8971 (mmm) REVERT: C 88 ASP cc_start: 0.7751 (t0) cc_final: 0.7452 (t0) REVERT: D 17 ARG cc_start: 0.9029 (ppp80) cc_final: 0.8631 (ptm-80) REVERT: D 32 ARG cc_start: 0.8853 (mtm180) cc_final: 0.8282 (mtp180) REVERT: D 68 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6913 (tm-30) REVERT: D 81 ASP cc_start: 0.8397 (m-30) cc_final: 0.7971 (m-30) REVERT: D 90 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7072 (p) REVERT: D 93 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8066 (tm-30) REVERT: D 100 ASN cc_start: 0.8514 (t0) cc_final: 0.8278 (t0) REVERT: D 135 ASP cc_start: 0.8325 (m-30) cc_final: 0.7851 (m-30) REVERT: B 29 MET cc_start: 0.9052 (mpp) cc_final: 0.8827 (mpp) REVERT: B 59 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8622 (mmmt) REVERT: B 63 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8869 (tmm-80) REVERT: L 482 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: L 486 LEU cc_start: 0.8534 (tm) cc_final: 0.8236 (mp) REVERT: L 502 ASP cc_start: 0.7856 (m-30) cc_final: 0.7418 (p0) REVERT: I 479 ASN cc_start: 0.8821 (t0) cc_final: 0.8521 (t0) REVERT: I 484 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8253 (mm-30) REVERT: I 495 ASP cc_start: 0.8596 (t70) cc_final: 0.8253 (t0) REVERT: P 88 ASP cc_start: 0.8332 (t0) cc_final: 0.7974 (t0) REVERT: P 123 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8452 (tptm) REVERT: N 1 MET cc_start: 0.7288 (tpt) cc_final: 0.6692 (tpp) REVERT: N 3 MET cc_start: 0.7111 (tpp) cc_final: 0.6755 (tpp) REVERT: N 14 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6991 (tm-30) REVERT: N 117 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8113 (tm-30) REVERT: M 17 ARG cc_start: 0.8994 (ppp80) cc_final: 0.8774 (ptm-80) REVERT: M 25 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8609 (mm-40) REVERT: M 32 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8545 (mmm-85) REVERT: M 59 LYS cc_start: 0.9070 (tptp) cc_final: 0.8863 (tptp) REVERT: M 93 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8505 (tm-30) REVERT: O 59 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8539 (mmmt) REVERT: O 60 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8322 (mm-30) REVERT: O 63 ARG cc_start: 0.9181 (ttt-90) cc_final: 0.8477 (ttp80) REVERT: O 103 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: V 502 ASP cc_start: 0.8315 (m-30) cc_final: 0.7317 (p0) REVERT: U 479 ASN cc_start: 0.8577 (t0) cc_final: 0.8239 (t0) REVERT: U 495 ASP cc_start: 0.8884 (p0) cc_final: 0.8651 (p0) REVERT: U 496 PHE cc_start: 0.8704 (m-80) cc_final: 0.8407 (m-10) REVERT: T 88 ASP cc_start: 0.8347 (t0) cc_final: 0.8056 (t0) REVERT: R 29 MET cc_start: 0.8965 (mmm) cc_final: 0.8275 (tpt) REVERT: R 63 ARG cc_start: 0.9278 (mtp-110) cc_final: 0.9033 (ttm110) REVERT: R 66 MET cc_start: 0.8935 (mmm) cc_final: 0.8735 (mmm) REVERT: R 107 ARG cc_start: 0.6925 (mmt90) cc_final: 0.6451 (mmt90) REVERT: Q 14 GLU cc_start: 0.9315 (tp30) cc_final: 0.8808 (tp30) REVERT: Q 29 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: Q 93 GLN cc_start: 0.8614 (pp30) cc_final: 0.7962 (pp30) REVERT: Q 134 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8046 (tm-30) REVERT: Q 136 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8490 (pp20) REVERT: S 81 ASP cc_start: 0.8077 (t0) cc_final: 0.7729 (t0) REVERT: W 479 ASN cc_start: 0.8678 (t0) cc_final: 0.8396 (t0) REVERT: W 480 ASP cc_start: 0.8781 (p0) cc_final: 0.8530 (p0) REVERT: W 496 PHE cc_start: 0.8607 (m-80) cc_final: 0.8333 (m-10) REVERT: E 59 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8681 (mmmt) REVERT: E 88 ASP cc_start: 0.8227 (t0) cc_final: 0.7833 (t0) REVERT: G 3 MET cc_start: 0.7128 (mmm) cc_final: 0.6894 (tpp) REVERT: G 25 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8294 (mm-40) REVERT: G 48 ASN cc_start: 0.9253 (t0) cc_final: 0.8945 (p0) REVERT: G 68 GLN cc_start: 0.7591 (mt0) cc_final: 0.7174 (mp10) REVERT: H 17 ARG cc_start: 0.8989 (ppp80) cc_final: 0.8573 (ptm-80) REVERT: H 32 ARG cc_start: 0.8974 (mmm-85) cc_final: 0.8655 (mmm-85) REVERT: H 56 TYR cc_start: 0.9038 (m-80) cc_final: 0.8642 (m-80) REVERT: H 60 GLU cc_start: 0.8968 (mp0) cc_final: 0.8605 (mp0) REVERT: H 68 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7315 (tm-30) REVERT: H 81 ASP cc_start: 0.8650 (m-30) cc_final: 0.8037 (m-30) REVERT: H 106 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.8015 (mtp180) REVERT: F 29 MET cc_start: 0.9091 (mpp) cc_final: 0.8843 (mpp) REVERT: F 53 ASP cc_start: 0.8874 (p0) cc_final: 0.8438 (p0) REVERT: F 101 ASN cc_start: 0.9131 (t0) cc_final: 0.8640 (t0) REVERT: F 103 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: F 123 LYS cc_start: 0.8948 (tppp) cc_final: 0.8552 (tptp) REVERT: K 495 ASP cc_start: 0.8898 (t0) cc_final: 0.8528 (t0) REVERT: K 496 PHE cc_start: 0.8932 (m-80) cc_final: 0.8505 (m-80) REVERT: K 500 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8621 (tp30) REVERT: K 503 ASP cc_start: 0.9399 (p0) cc_final: 0.8789 (p0) outliers start: 114 outliers final: 60 residues processed: 624 average time/residue: 1.1296 time to fit residues: 802.8706 Evaluate side-chains 598 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 526 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 482 GLU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 228 optimal weight: 0.7980 chunk 191 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 103 GLN C 42 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN T 42 HIS ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 102 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.113559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.089298 restraints weight = 60271.184| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 5.03 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20223 Z= 0.168 Angle : 0.698 10.289 27351 Z= 0.349 Chirality : 0.045 0.176 2905 Planarity : 0.004 0.053 3638 Dihedral : 4.951 58.451 2715 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.33 % Allowed : 32.82 % Favored : 61.85 % 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: 1.12 (0.18), residues: 2415 helix: 2.00 (0.20), residues: 618 sheet: -0.09 (0.18), residues: 724 loop : 0.81 (0.22), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.010 0.001 HIS G 62 PHE 0.018 0.002 PHE O 131 TYR 0.026 0.002 TYR R 40 ARG 0.009 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 892) hydrogen bonds : angle 4.87708 ( 2490) covalent geometry : bond 0.00395 (20223) covalent geometry : angle 0.69774 (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 653 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 538 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7585 (t0) cc_final: 0.7123 (t0) REVERT: A 88 ASP cc_start: 0.8457 (t0) cc_final: 0.8148 (t0) REVERT: A 123 LYS cc_start: 0.9242 (tttm) cc_final: 0.9019 (mmmt) REVERT: A 132 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7470 (mtp85) REVERT: C 36 LYS cc_start: 0.8940 (tmmt) cc_final: 0.8500 (mmpt) REVERT: C 63 ARG cc_start: 0.9352 (ptm160) cc_final: 0.9026 (ptm-80) REVERT: C 66 MET cc_start: 0.9225 (mmm) cc_final: 0.8987 (mmm) REVERT: C 88 ASP cc_start: 0.7773 (t0) cc_final: 0.7472 (t0) REVERT: D 32 ARG cc_start: 0.8841 (mtm180) cc_final: 0.8299 (mtp180) REVERT: D 68 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7087 (tm-30) REVERT: D 81 ASP cc_start: 0.8380 (m-30) cc_final: 0.7819 (m-30) REVERT: D 90 VAL cc_start: 0.7482 (OUTLIER) cc_final: 0.7028 (p) REVERT: D 93 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7776 (tm-30) REVERT: D 95 MET cc_start: 0.6949 (mtt) cc_final: 0.6708 (mtt) REVERT: D 135 ASP cc_start: 0.8338 (m-30) cc_final: 0.7879 (m-30) REVERT: B 59 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8608 (mmmt) REVERT: B 63 ARG cc_start: 0.9160 (OUTLIER) cc_final: 0.8869 (tmm-80) REVERT: B 101 ASN cc_start: 0.9319 (t0) cc_final: 0.8709 (t0) REVERT: L 486 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8268 (mp) REVERT: L 502 ASP cc_start: 0.7880 (m-30) cc_final: 0.7397 (t0) REVERT: I 479 ASN cc_start: 0.8822 (t0) cc_final: 0.8546 (t0) REVERT: I 495 ASP cc_start: 0.8627 (t70) cc_final: 0.8273 (t0) REVERT: P 88 ASP cc_start: 0.8469 (t0) cc_final: 0.7819 (t0) REVERT: P 102 ASN cc_start: 0.8854 (t0) cc_final: 0.8395 (t0) REVERT: P 123 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8480 (tptm) REVERT: N 1 MET cc_start: 0.7229 (tpt) cc_final: 0.6628 (tpp) REVERT: N 3 MET cc_start: 0.7185 (tpp) cc_final: 0.6801 (tpp) REVERT: N 14 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6950 (tm-30) REVERT: N 29 MET cc_start: 0.8910 (tpt) cc_final: 0.8393 (tpt) REVERT: N 117 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8140 (tm-30) REVERT: M 17 ARG cc_start: 0.9029 (ppp80) cc_final: 0.8747 (ptm-80) REVERT: M 25 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8607 (mm-40) REVERT: M 32 ARG cc_start: 0.8987 (mmm-85) cc_final: 0.8526 (mmm-85) REVERT: M 59 LYS cc_start: 0.9063 (tptp) cc_final: 0.8842 (tptp) REVERT: M 66 MET cc_start: 0.8983 (mmp) cc_final: 0.8669 (mmm) REVERT: M 93 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8527 (tm-30) REVERT: O 60 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8323 (mm-30) REVERT: O 63 ARG cc_start: 0.9183 (ttt-90) cc_final: 0.8476 (ttp80) REVERT: O 103 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: V 502 ASP cc_start: 0.8382 (m-30) cc_final: 0.7383 (p0) REVERT: U 479 ASN cc_start: 0.8611 (t0) cc_final: 0.8293 (t0) REVERT: U 495 ASP cc_start: 0.8904 (p0) cc_final: 0.8663 (p0) REVERT: U 496 PHE cc_start: 0.8551 (m-80) cc_final: 0.8001 (m-10) REVERT: U 500 GLU cc_start: 0.8917 (tt0) cc_final: 0.8687 (tt0) REVERT: T 76 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.8108 (tptp) REVERT: T 88 ASP cc_start: 0.8398 (t0) cc_final: 0.8128 (t0) REVERT: R 29 MET cc_start: 0.8960 (mmm) cc_final: 0.8345 (tpt) REVERT: R 63 ARG cc_start: 0.9270 (mtp-110) cc_final: 0.9020 (ttm110) REVERT: R 66 MET cc_start: 0.8976 (mmm) cc_final: 0.8760 (mmm) REVERT: R 103 GLN cc_start: 0.8405 (mp10) cc_final: 0.8180 (mp10) REVERT: Q 14 GLU cc_start: 0.9335 (tp30) cc_final: 0.8887 (tp30) REVERT: Q 93 GLN cc_start: 0.8641 (pp30) cc_final: 0.7954 (pp30) REVERT: Q 134 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7761 (tm130) REVERT: Q 136 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8558 (pp20) REVERT: S 63 ARG cc_start: 0.9190 (tmm-80) cc_final: 0.8967 (ttp80) REVERT: W 479 ASN cc_start: 0.8661 (t0) cc_final: 0.8377 (t0) REVERT: W 480 ASP cc_start: 0.8761 (p0) cc_final: 0.8517 (p0) REVERT: W 496 PHE cc_start: 0.8705 (m-80) cc_final: 0.8429 (m-10) REVERT: E 59 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8695 (mmmt) REVERT: E 76 LYS cc_start: 0.7955 (tptt) cc_final: 0.7141 (tptp) REVERT: E 88 ASP cc_start: 0.8306 (t0) cc_final: 0.7921 (t0) REVERT: G 25 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8297 (mm-40) REVERT: G 48 ASN cc_start: 0.9262 (t0) cc_final: 0.8948 (p0) REVERT: G 68 GLN cc_start: 0.7574 (mt0) cc_final: 0.7150 (mp10) REVERT: H 17 ARG cc_start: 0.8975 (ppp80) cc_final: 0.8537 (ptm-80) REVERT: H 56 TYR cc_start: 0.9035 (m-80) cc_final: 0.8651 (m-80) REVERT: H 60 GLU cc_start: 0.8941 (mp0) cc_final: 0.8568 (mp0) REVERT: H 68 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7492 (tm-30) REVERT: H 81 ASP cc_start: 0.8619 (m-30) cc_final: 0.8050 (m-30) REVERT: H 106 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: F 29 MET cc_start: 0.9060 (mpp) cc_final: 0.8781 (mpp) REVERT: F 53 ASP cc_start: 0.8878 (p0) cc_final: 0.8449 (p0) REVERT: F 101 ASN cc_start: 0.9133 (t0) cc_final: 0.8641 (t0) REVERT: F 103 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: F 123 LYS cc_start: 0.8932 (tppp) cc_final: 0.8530 (tptp) REVERT: J 495 ASP cc_start: 0.8188 (m-30) cc_final: 0.7873 (p0) REVERT: K 495 ASP cc_start: 0.8892 (t0) cc_final: 0.8510 (t0) REVERT: K 496 PHE cc_start: 0.8981 (m-80) cc_final: 0.8594 (m-80) REVERT: K 500 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8586 (tp30) outliers start: 115 outliers final: 61 residues processed: 609 average time/residue: 1.1307 time to fit residues: 784.1660 Evaluate side-chains 590 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 517 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain V residue 483 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain S residue 137 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 135 ASP Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 2 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 69 optimal weight: 0.0570 chunk 105 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 42 HIS ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN M 110 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN T 68 GLN ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 68 GLN S 93 GLN S 102 ASN S 128 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS H 69 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3913 r_free = 0.3913 target = 0.116888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092253 restraints weight = 72458.755| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 5.51 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20223 Z= 0.134 Angle : 0.726 12.623 27351 Z= 0.356 Chirality : 0.045 0.184 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.758 59.465 2713 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.36 % Allowed : 34.35 % Favored : 61.29 % 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: 1.16 (0.18), residues: 2415 helix: 1.95 (0.20), residues: 618 sheet: -0.08 (0.18), residues: 736 loop : 0.92 (0.23), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP W 509 HIS 0.008 0.001 HIS O 79 PHE 0.016 0.002 PHE O 131 TYR 0.017 0.001 TYR G 20 ARG 0.011 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 892) hydrogen bonds : angle 4.82107 ( 2490) covalent geometry : bond 0.00314 (20223) covalent geometry : angle 0.72625 (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 674 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 580 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8186 (tppp) cc_final: 0.7689 (tptt) REVERT: A 81 ASP cc_start: 0.7609 (t0) cc_final: 0.7189 (t0) REVERT: A 88 ASP cc_start: 0.8497 (t0) cc_final: 0.8124 (t0) REVERT: A 132 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7227 (mtp85) REVERT: C 29 MET cc_start: 0.8957 (ttm) cc_final: 0.8055 (ttm) REVERT: C 32 ARG cc_start: 0.8871 (ttp80) cc_final: 0.8495 (ttm170) REVERT: C 63 ARG cc_start: 0.9362 (ptm160) cc_final: 0.9020 (ptm-80) REVERT: C 66 MET cc_start: 0.9217 (mmm) cc_final: 0.8983 (mmm) REVERT: C 88 ASP cc_start: 0.7842 (t0) cc_final: 0.7520 (t0) REVERT: D 17 ARG cc_start: 0.8970 (ppp80) cc_final: 0.8703 (ptm-80) REVERT: D 32 ARG cc_start: 0.8846 (mtm180) cc_final: 0.8144 (mtp180) REVERT: D 36 LYS cc_start: 0.8882 (tppt) cc_final: 0.8312 (tppt) REVERT: D 37 ASN cc_start: 0.9339 (t0) cc_final: 0.8933 (p0) REVERT: D 68 GLN cc_start: 0.7317 (tm-30) cc_final: 0.7033 (tm-30) REVERT: D 81 ASP cc_start: 0.8393 (m-30) cc_final: 0.7732 (m-30) REVERT: D 93 GLN cc_start: 0.8573 (tm-30) cc_final: 0.7657 (tm-30) REVERT: D 100 ASN cc_start: 0.8476 (t0) cc_final: 0.8232 (t0) REVERT: D 135 ASP cc_start: 0.8255 (m-30) cc_final: 0.7797 (m-30) REVERT: B 59 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8600 (mmmt) REVERT: B 63 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8857 (tmm-80) REVERT: B 101 ASN cc_start: 0.9253 (t0) cc_final: 0.8599 (t0) REVERT: B 109 MET cc_start: 0.7745 (mtt) cc_final: 0.7535 (mtt) REVERT: L 486 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8220 (mp) REVERT: L 502 ASP cc_start: 0.7869 (m-30) cc_final: 0.7381 (t0) REVERT: I 479 ASN cc_start: 0.8675 (t0) cc_final: 0.8396 (t0) REVERT: P 88 ASP cc_start: 0.8330 (t0) cc_final: 0.7854 (t0) REVERT: P 102 ASN cc_start: 0.8814 (t0) cc_final: 0.8341 (t0) REVERT: P 123 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8446 (tptm) REVERT: N 1 MET cc_start: 0.7237 (tpt) cc_final: 0.6671 (tpp) REVERT: N 3 MET cc_start: 0.6968 (tpp) cc_final: 0.6586 (tpp) REVERT: N 14 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6932 (tm-30) REVERT: N 29 MET cc_start: 0.8890 (tpt) cc_final: 0.8400 (tpt) REVERT: N 36 LYS cc_start: 0.8904 (pptt) cc_final: 0.8264 (mmpt) REVERT: N 37 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7548 (t0) REVERT: N 62 HIS cc_start: 0.8768 (t-90) cc_final: 0.8554 (t-90) REVERT: N 117 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8170 (tm-30) REVERT: N 123 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8115 (tppp) REVERT: M 17 ARG cc_start: 0.8992 (ppp80) cc_final: 0.8708 (ptm-80) REVERT: M 25 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8596 (mm-40) REVERT: M 32 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: M 66 MET cc_start: 0.8923 (mmp) cc_final: 0.8624 (mmm) REVERT: M 93 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8254 (tm-30) REVERT: M 95 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7160 (mtt) REVERT: M 103 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: O 63 ARG cc_start: 0.9168 (ttt-90) cc_final: 0.8469 (ttp80) REVERT: O 103 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: V 502 ASP cc_start: 0.8376 (m-30) cc_final: 0.7341 (p0) REVERT: U 479 ASN cc_start: 0.8601 (t0) cc_final: 0.8272 (t0) REVERT: U 495 ASP cc_start: 0.8877 (p0) cc_final: 0.8658 (p0) REVERT: U 496 PHE cc_start: 0.8538 (m-80) cc_final: 0.8051 (m-10) REVERT: T 76 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8117 (tptp) REVERT: T 88 ASP cc_start: 0.8363 (t0) cc_final: 0.8078 (t0) REVERT: R 29 MET cc_start: 0.8942 (mmm) cc_final: 0.8294 (tpt) REVERT: R 63 ARG cc_start: 0.9276 (mtp-110) cc_final: 0.9027 (ttm110) REVERT: R 66 MET cc_start: 0.9004 (mmm) cc_final: 0.8766 (mmm) REVERT: R 103 GLN cc_start: 0.8376 (mp10) cc_final: 0.8153 (mp10) REVERT: Q 14 GLU cc_start: 0.9324 (tp30) cc_final: 0.8870 (tp30) REVERT: Q 93 GLN cc_start: 0.8647 (pp30) cc_final: 0.7947 (pp30) REVERT: Q 109 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7885 (ttt) REVERT: Q 134 GLN cc_start: 0.8242 (tm-30) cc_final: 0.8030 (tm-30) REVERT: Q 136 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8554 (pp20) REVERT: S 60 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8426 (mm-30) REVERT: S 63 ARG cc_start: 0.9179 (tmm-80) cc_final: 0.8918 (ttp80) REVERT: S 81 ASP cc_start: 0.8064 (t0) cc_final: 0.7714 (t0) REVERT: X 484 GLU cc_start: 0.8005 (mp0) cc_final: 0.7714 (pm20) REVERT: W 479 ASN cc_start: 0.8664 (t0) cc_final: 0.8385 (t0) REVERT: W 480 ASP cc_start: 0.8727 (p0) cc_final: 0.8475 (p0) REVERT: W 496 PHE cc_start: 0.8672 (m-80) cc_final: 0.8380 (m-10) REVERT: E 59 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8702 (mmmt) REVERT: E 88 ASP cc_start: 0.8324 (t0) cc_final: 0.7947 (t0) REVERT: G 3 MET cc_start: 0.6872 (tpt) cc_final: 0.6534 (tpp) REVERT: G 25 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8265 (mm-40) REVERT: G 29 MET cc_start: 0.8841 (mmm) cc_final: 0.8550 (mtp) REVERT: G 48 ASN cc_start: 0.9276 (t0) cc_final: 0.9015 (p0) REVERT: G 68 GLN cc_start: 0.7432 (mt0) cc_final: 0.7051 (mp10) REVERT: H 17 ARG cc_start: 0.8963 (ppp80) cc_final: 0.8522 (ptm-80) REVERT: H 32 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: H 56 TYR cc_start: 0.9040 (m-80) cc_final: 0.8629 (m-80) REVERT: H 60 GLU cc_start: 0.8985 (mp0) cc_final: 0.8553 (mp0) REVERT: H 81 ASP cc_start: 0.8621 (m-30) cc_final: 0.8038 (m-30) REVERT: H 106 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7986 (mtp180) REVERT: F 29 MET cc_start: 0.9082 (mpp) cc_final: 0.8835 (mpp) REVERT: F 53 ASP cc_start: 0.8850 (p0) cc_final: 0.8433 (p0) REVERT: F 103 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7492 (mp10) REVERT: F 123 LYS cc_start: 0.8954 (tppp) cc_final: 0.8563 (tptp) REVERT: J 488 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7765 (p) REVERT: J 495 ASP cc_start: 0.8181 (m-30) cc_final: 0.7948 (p0) REVERT: K 495 ASP cc_start: 0.8860 (t0) cc_final: 0.8479 (t0) REVERT: K 500 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8452 (tp30) outliers start: 94 outliers final: 44 residues processed: 631 average time/residue: 1.1321 time to fit residues: 812.2953 Evaluate side-chains 601 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 541 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 109 MET Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 204 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 42 HIS ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.115154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.090754 restraints weight = 63777.181| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.24 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20223 Z= 0.157 Angle : 0.750 12.491 27351 Z= 0.370 Chirality : 0.046 0.200 2905 Planarity : 0.004 0.051 3638 Dihedral : 4.789 59.865 2711 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.54 % Allowed : 34.91 % Favored : 60.55 % 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: 1.17 (0.18), residues: 2415 helix: 1.91 (0.20), residues: 618 sheet: -0.06 (0.18), residues: 728 loop : 0.93 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP U 509 HIS 0.015 0.001 HIS O 79 PHE 0.027 0.002 PHE Q 15 TYR 0.028 0.002 TYR R 40 ARG 0.011 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03479 ( 892) hydrogen bonds : angle 4.84978 ( 2490) covalent geometry : bond 0.00371 (20223) covalent geometry : angle 0.74986 (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 646 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 548 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8229 (tppp) cc_final: 0.8004 (tppt) REVERT: A 81 ASP cc_start: 0.7649 (t0) cc_final: 0.7177 (t0) REVERT: A 88 ASP cc_start: 0.8520 (t0) cc_final: 0.8150 (t0) REVERT: A 132 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: C 36 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8553 (mmpt) REVERT: C 63 ARG cc_start: 0.9375 (ptm160) cc_final: 0.9021 (ptm-80) REVERT: C 66 MET cc_start: 0.9220 (mmm) cc_final: 0.8970 (mmm) REVERT: C 88 ASP cc_start: 0.7842 (t0) cc_final: 0.7513 (t0) REVERT: C 107 ARG cc_start: 0.7569 (mmt90) cc_final: 0.7268 (mmt90) REVERT: D 17 ARG cc_start: 0.8962 (ppp80) cc_final: 0.8655 (ptm-80) REVERT: D 32 ARG cc_start: 0.8852 (mtm180) cc_final: 0.8167 (mtp180) REVERT: D 63 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8285 (ttm110) REVERT: D 68 GLN cc_start: 0.7367 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 78 ARG cc_start: 0.8620 (tpm170) cc_final: 0.7946 (tpp-160) REVERT: D 81 ASP cc_start: 0.8407 (m-30) cc_final: 0.7643 (m-30) REVERT: D 93 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7469 (tm-30) REVERT: D 100 ASN cc_start: 0.8464 (t0) cc_final: 0.8224 (t0) REVERT: D 135 ASP cc_start: 0.8255 (m-30) cc_final: 0.7816 (m-30) REVERT: B 59 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8618 (mmmt) REVERT: B 63 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8852 (tmm-80) REVERT: B 101 ASN cc_start: 0.9277 (t0) cc_final: 0.8620 (t0) REVERT: B 109 MET cc_start: 0.8055 (mtt) cc_final: 0.7759 (mtt) REVERT: L 486 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8220 (mp) REVERT: L 502 ASP cc_start: 0.7886 (m-30) cc_final: 0.7417 (t0) REVERT: I 479 ASN cc_start: 0.8724 (t0) cc_final: 0.8432 (t0) REVERT: I 497 LEU cc_start: 0.9031 (mm) cc_final: 0.8692 (pp) REVERT: P 88 ASP cc_start: 0.8529 (t0) cc_final: 0.7898 (t0) REVERT: P 102 ASN cc_start: 0.8850 (t0) cc_final: 0.8378 (t0) REVERT: P 123 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8487 (tptm) REVERT: P 132 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7619 (mtp85) REVERT: N 1 MET cc_start: 0.7254 (tpt) cc_final: 0.6694 (tpp) REVERT: N 3 MET cc_start: 0.7046 (tpp) cc_final: 0.6659 (tpp) REVERT: N 14 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7049 (tm-30) REVERT: N 29 MET cc_start: 0.8891 (tpt) cc_final: 0.8366 (tpt) REVERT: N 37 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: N 68 GLN cc_start: 0.7772 (mp10) cc_final: 0.7486 (mp10) REVERT: N 107 ARG cc_start: 0.7288 (mmt90) cc_final: 0.6967 (mmt90) REVERT: N 117 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7972 (tm-30) REVERT: N 123 LYS cc_start: 0.8335 (ttpt) cc_final: 0.8082 (tppp) REVERT: M 17 ARG cc_start: 0.8993 (ppp80) cc_final: 0.8700 (ppp80) REVERT: M 25 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8622 (mm-40) REVERT: M 32 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8613 (mmm-85) REVERT: M 66 MET cc_start: 0.8952 (mmp) cc_final: 0.8670 (mmm) REVERT: M 93 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8083 (tm-30) REVERT: M 103 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: O 63 ARG cc_start: 0.9102 (ttt-90) cc_final: 0.8488 (ttp80) REVERT: O 103 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7151 (mp10) REVERT: V 477 ASP cc_start: 0.8531 (p0) cc_final: 0.8296 (p0) REVERT: V 502 ASP cc_start: 0.8413 (m-30) cc_final: 0.7409 (p0) REVERT: U 479 ASN cc_start: 0.8587 (t0) cc_final: 0.8264 (t0) REVERT: U 495 ASP cc_start: 0.8861 (p0) cc_final: 0.8635 (p0) REVERT: U 496 PHE cc_start: 0.8500 (m-80) cc_final: 0.7975 (m-10) REVERT: U 500 GLU cc_start: 0.8978 (tt0) cc_final: 0.8761 (tt0) REVERT: T 76 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8148 (tptp) REVERT: T 88 ASP cc_start: 0.8341 (t0) cc_final: 0.8035 (t0) REVERT: R 29 MET cc_start: 0.8950 (mmm) cc_final: 0.8295 (tpt) REVERT: R 37 ASN cc_start: 0.8457 (t0) cc_final: 0.8075 (m-40) REVERT: R 63 ARG cc_start: 0.9289 (mtp-110) cc_final: 0.9038 (ttm110) REVERT: R 66 MET cc_start: 0.9040 (mmm) cc_final: 0.8790 (mmm) REVERT: R 103 GLN cc_start: 0.8383 (mp10) cc_final: 0.8167 (mp10) REVERT: Q 14 GLU cc_start: 0.9324 (tp30) cc_final: 0.8739 (tp30) REVERT: Q 93 GLN cc_start: 0.8687 (pp30) cc_final: 0.7974 (pp30) REVERT: Q 109 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7957 (ttt) REVERT: Q 134 GLN cc_start: 0.8250 (tm-30) cc_final: 0.8029 (tm-30) REVERT: Q 136 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8612 (pp20) REVERT: S 81 ASP cc_start: 0.8030 (t0) cc_final: 0.7672 (t0) REVERT: W 479 ASN cc_start: 0.8645 (t0) cc_final: 0.8358 (t0) REVERT: W 480 ASP cc_start: 0.8696 (p0) cc_final: 0.8459 (p0) REVERT: W 496 PHE cc_start: 0.8703 (m-80) cc_final: 0.8383 (m-10) REVERT: E 59 LYS cc_start: 0.9109 (mmmm) cc_final: 0.8713 (mmmt) REVERT: E 88 ASP cc_start: 0.8416 (t0) cc_final: 0.8004 (t0) REVERT: G 3 MET cc_start: 0.6974 (tpt) cc_final: 0.6622 (tpp) REVERT: G 48 ASN cc_start: 0.9259 (t0) cc_final: 0.9011 (p0) REVERT: G 68 GLN cc_start: 0.7398 (mt0) cc_final: 0.6992 (mp10) REVERT: H 17 ARG cc_start: 0.8993 (ppp80) cc_final: 0.8590 (ppp80) REVERT: H 32 ARG cc_start: 0.8968 (mmm-85) cc_final: 0.8729 (mmm-85) REVERT: H 36 LYS cc_start: 0.8735 (tppt) cc_final: 0.8460 (ttmm) REVERT: H 60 GLU cc_start: 0.8989 (mp0) cc_final: 0.8672 (mp0) REVERT: H 81 ASP cc_start: 0.8617 (m-30) cc_final: 0.8038 (m-30) REVERT: H 106 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8013 (mtp180) REVERT: F 53 ASP cc_start: 0.8840 (p0) cc_final: 0.8418 (p0) REVERT: F 101 ASN cc_start: 0.9122 (t0) cc_final: 0.8649 (t0) REVERT: F 103 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: F 123 LYS cc_start: 0.8927 (tppp) cc_final: 0.8529 (tptp) REVERT: J 495 ASP cc_start: 0.8199 (m-30) cc_final: 0.7948 (p0) REVERT: K 479 ASN cc_start: 0.8928 (t0) cc_final: 0.8630 (t0) REVERT: K 480 ASP cc_start: 0.8925 (t0) cc_final: 0.8662 (t0) REVERT: K 495 ASP cc_start: 0.8894 (t0) cc_final: 0.8529 (t0) REVERT: K 496 PHE cc_start: 0.9044 (m-80) cc_final: 0.8719 (m-80) REVERT: K 500 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8549 (tp30) outliers start: 98 outliers final: 54 residues processed: 608 average time/residue: 1.1609 time to fit residues: 802.4694 Evaluate side-chains 606 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 537 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 132 ARG Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 37 ASN Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 95 MET Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 109 MET Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 33 PHE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 500 GLU 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: 6.9990 chunk 138 optimal weight: 6.9990 chunk 120 optimal weight: 0.3980 chunk 182 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 197 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 219 optimal weight: 0.6980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 103 GLN C 42 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS Q 101 ASN S 48 ASN ** S 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.115543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091225 restraints weight = 60101.055| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 5.09 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20223 Z= 0.155 Angle : 0.770 12.819 27351 Z= 0.378 Chirality : 0.046 0.207 2905 Planarity : 0.004 0.051 3638 Dihedral : 4.805 59.615 2711 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.66 % Allowed : 36.44 % Favored : 59.90 % 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: 1.18 (0.18), residues: 2415 helix: 1.85 (0.20), residues: 618 sheet: -0.08 (0.18), residues: 736 loop : 1.01 (0.23), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP U 509 HIS 0.014 0.001 HIS O 79 PHE 0.026 0.002 PHE Q 15 TYR 0.023 0.001 TYR C 40 ARG 0.012 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 892) hydrogen bonds : angle 4.87193 ( 2490) covalent geometry : bond 0.00367 (20223) covalent geometry : angle 0.76982 (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 608 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 529 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 LYS cc_start: 0.8196 (tppp) cc_final: 0.7991 (tppt) REVERT: A 81 ASP cc_start: 0.7636 (t0) cc_final: 0.7166 (t0) REVERT: A 88 ASP cc_start: 0.8517 (t0) cc_final: 0.8118 (t0) REVERT: A 132 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7497 (mtp85) REVERT: C 36 LYS cc_start: 0.8951 (tmmt) cc_final: 0.8588 (mmpt) REVERT: C 63 ARG cc_start: 0.9380 (ptm160) cc_final: 0.9030 (ptm-80) REVERT: C 66 MET cc_start: 0.9208 (mmm) cc_final: 0.8959 (mmm) REVERT: C 88 ASP cc_start: 0.7827 (t0) cc_final: 0.7491 (t0) REVERT: D 32 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8122 (mtp180) REVERT: D 63 ARG cc_start: 0.8548 (ttm110) cc_final: 0.8321 (ttm110) REVERT: D 68 GLN cc_start: 0.7366 (tm-30) cc_final: 0.7048 (tm-30) REVERT: D 78 ARG cc_start: 0.8590 (tpm170) cc_final: 0.7963 (tpp-160) REVERT: D 81 ASP cc_start: 0.8346 (m-30) cc_final: 0.7634 (m-30) REVERT: D 93 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7441 (tm-30) REVERT: D 100 ASN cc_start: 0.8455 (t0) cc_final: 0.8209 (t0) REVERT: D 135 ASP cc_start: 0.8244 (m-30) cc_final: 0.7802 (m-30) REVERT: B 59 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8623 (mmmt) REVERT: B 63 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8854 (tmm-80) REVERT: B 101 ASN cc_start: 0.9267 (t0) cc_final: 0.8594 (t0) REVERT: B 109 MET cc_start: 0.8020 (mtt) cc_final: 0.7776 (mtt) REVERT: L 486 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8227 (mp) REVERT: L 502 ASP cc_start: 0.7890 (m-30) cc_final: 0.7424 (t0) REVERT: I 479 ASN cc_start: 0.8729 (t0) cc_final: 0.8419 (t0) REVERT: I 497 LEU cc_start: 0.9125 (mm) cc_final: 0.8800 (pp) REVERT: P 88 ASP cc_start: 0.8537 (t0) cc_final: 0.7904 (t0) REVERT: P 102 ASN cc_start: 0.8858 (t0) cc_final: 0.8400 (t0) REVERT: P 123 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8492 (tptm) REVERT: N 1 MET cc_start: 0.7248 (tpt) cc_final: 0.6687 (tpp) REVERT: N 3 MET cc_start: 0.7091 (tpp) cc_final: 0.6703 (tpp) REVERT: N 14 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7196 (tp30) REVERT: N 29 MET cc_start: 0.8921 (tpt) cc_final: 0.8360 (tpt) REVERT: N 68 GLN cc_start: 0.7862 (mp10) cc_final: 0.7510 (mp10) REVERT: N 109 MET cc_start: 0.8259 (mtp) cc_final: 0.7988 (mtp) REVERT: N 117 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8186 (tm-30) REVERT: N 123 LYS cc_start: 0.8322 (ttpt) cc_final: 0.8085 (tppp) REVERT: M 17 ARG cc_start: 0.8995 (ppp80) cc_final: 0.8709 (ppp80) REVERT: M 25 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8651 (mm-40) REVERT: M 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8555 (mmm-85) REVERT: M 66 MET cc_start: 0.8917 (mmp) cc_final: 0.8701 (mmm) REVERT: M 93 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8026 (tm-30) REVERT: M 103 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (mp10) REVERT: O 63 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8511 (ttp80) REVERT: O 103 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7202 (mp10) REVERT: V 477 ASP cc_start: 0.8509 (p0) cc_final: 0.8277 (p0) REVERT: V 502 ASP cc_start: 0.8386 (m-30) cc_final: 0.7480 (p0) REVERT: U 479 ASN cc_start: 0.8570 (t0) cc_final: 0.8249 (t0) REVERT: U 496 PHE cc_start: 0.8503 (m-80) cc_final: 0.8001 (m-10) REVERT: U 500 GLU cc_start: 0.8998 (tt0) cc_final: 0.8789 (tt0) REVERT: T 76 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8162 (tptp) REVERT: T 88 ASP cc_start: 0.8341 (t0) cc_final: 0.8003 (t0) REVERT: R 29 MET cc_start: 0.8947 (mmm) cc_final: 0.8271 (tpt) REVERT: R 63 ARG cc_start: 0.9303 (mtp-110) cc_final: 0.9050 (ttm110) REVERT: R 66 MET cc_start: 0.9069 (mmm) cc_final: 0.8813 (mmm) REVERT: R 103 GLN cc_start: 0.8403 (mp10) cc_final: 0.8189 (mp10) REVERT: Q 14 GLU cc_start: 0.9309 (tp30) cc_final: 0.8868 (tp30) REVERT: Q 93 GLN cc_start: 0.8642 (pp30) cc_final: 0.7998 (pp30) REVERT: Q 134 GLN cc_start: 0.8275 (tm-30) cc_final: 0.8074 (tm-30) REVERT: Q 136 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: W 479 ASN cc_start: 0.8644 (t0) cc_final: 0.8361 (t0) REVERT: W 480 ASP cc_start: 0.8692 (p0) cc_final: 0.8457 (p0) REVERT: W 496 PHE cc_start: 0.8695 (m-80) cc_final: 0.8356 (m-10) REVERT: E 59 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8738 (mmtt) REVERT: E 69 ASN cc_start: 0.8197 (t0) cc_final: 0.7974 (p0) REVERT: E 76 LYS cc_start: 0.7899 (tptt) cc_final: 0.7162 (tptp) REVERT: E 88 ASP cc_start: 0.8439 (t0) cc_final: 0.8032 (t0) REVERT: G 3 MET cc_start: 0.6996 (tpt) cc_final: 0.6666 (tpp) REVERT: G 48 ASN cc_start: 0.9255 (t0) cc_final: 0.8962 (p0) REVERT: G 68 GLN cc_start: 0.7410 (mt0) cc_final: 0.6965 (mp10) REVERT: H 17 ARG cc_start: 0.8995 (ppp80) cc_final: 0.8597 (ppp80) REVERT: H 32 ARG cc_start: 0.9015 (mmm-85) cc_final: 0.8776 (mmm-85) REVERT: H 36 LYS cc_start: 0.8775 (tppt) cc_final: 0.8499 (ttmm) REVERT: H 60 GLU cc_start: 0.8966 (mp0) cc_final: 0.8628 (mp0) REVERT: H 81 ASP cc_start: 0.8592 (m-30) cc_final: 0.8043 (m-30) REVERT: H 106 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8028 (mtp180) REVERT: F 29 MET cc_start: 0.9081 (mpp) cc_final: 0.8852 (mpp) REVERT: F 53 ASP cc_start: 0.8850 (p0) cc_final: 0.8429 (p0) REVERT: F 103 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: F 123 LYS cc_start: 0.8920 (tppp) cc_final: 0.8521 (tptp) REVERT: J 495 ASP cc_start: 0.8227 (m-30) cc_final: 0.7999 (p0) REVERT: K 479 ASN cc_start: 0.8909 (t0) cc_final: 0.8616 (t0) REVERT: K 480 ASP cc_start: 0.8901 (t0) cc_final: 0.8633 (t0) REVERT: K 495 ASP cc_start: 0.8880 (t0) cc_final: 0.8511 (t0) REVERT: K 496 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8823 (m-80) REVERT: K 500 GLU cc_start: 0.9104 (OUTLIER) cc_final: 0.8495 (tp30) outliers start: 79 outliers final: 50 residues processed: 581 average time/residue: 1.1483 time to fit residues: 761.0923 Evaluate side-chains 596 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 533 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain L residue 473 ILE Chi-restraints excluded: chain L residue 486 LEU Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS 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 10 LEU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain X residue 473 ILE Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain K residue 496 PHE Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 41 optimal weight: 0.3980 chunk 181 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS C 42 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 128 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.091677 restraints weight = 65907.548| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 5.27 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20223 Z= 0.147 Angle : 0.758 13.155 27351 Z= 0.373 Chirality : 0.046 0.206 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.795 59.330 2711 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.99 % Allowed : 35.88 % Favored : 60.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.18), residues: 2415 helix: 1.81 (0.20), residues: 618 sheet: -0.09 (0.18), residues: 736 loop : 1.04 (0.23), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP W 509 HIS 0.014 0.001 HIS O 79 PHE 0.025 0.002 PHE Q 15 TYR 0.028 0.002 TYR G 40 ARG 0.011 0.001 ARG M 63 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 892) hydrogen bonds : angle 4.85252 ( 2490) covalent geometry : bond 0.00346 (20223) covalent geometry : angle 0.75819 (27351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15271.10 seconds wall clock time: 263 minutes 45.30 seconds (15825.30 seconds total)