Starting phenix.real_space_refine on Tue Jun 17 05:02:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivs_60934/06_2025/9ivs_60934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivs_60934/06_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_60934/06_2025/9ivs_60934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivs_60934/06_2025/9ivs_60934.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivs_60934/06_2025/9ivs_60934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivs_60934/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "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: 12.50, per 1000 atoms: 0.63 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: 4.84 Conformation dependent library (CDL) restraints added in 2.5 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: 2.99 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: 7.33 Time building geometry restraints manager: 5.58 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: 3.080 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: 0.030 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 46.300 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.040 ------------------------------------------------------------------------------- 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 : 2.354 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: 1.2162 time to fit residues: 881.9772 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 : 2.163 ------------------------------------------------------------------------------- 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 = 0.117476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092689 restraints weight = 61567.684| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 5.20 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 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 = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- 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 : 2.370 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: 0.9136 (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: 0.9102 (OUTLIER) cc_final: 0.8897 (tm) REVERT: D 32 ARG cc_start: 0.8957 (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: 0.8375 (m-30) cc_final: 0.8110 (m-30) REVERT: B 29 MET cc_start: 0.9031 (mpp) cc_final: 0.8766 (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: 0.8382 (t0) cc_final: 0.8156 (t0) REVERT: I 496 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7499 (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: 0.8418 (ptp) REVERT: N 1 MET cc_start: 0.7379 (tpp) cc_final: 0.7038 (tpp) REVERT: N 14 GLU cc_start: 0.7536 (tm-30) cc_final: 0.6968 (tm-30) REVERT: N 29 MET cc_start: 0.8544 (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: 0.7017 (mmt90) REVERT: N 117 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8139 (tm-30) REVERT: M 25 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8642 (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: 0.8983 (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: 0.8103 (tppt) REVERT: O 36 LYS cc_start: 0.9095 (pmmt) cc_final: 0.8886 (pptt) REVERT: O 60 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8347 (mm-30) REVERT: O 63 ARG cc_start: 0.9152 (ttt-90) cc_final: 0.8474 (ttp80) REVERT: O 103 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6867 (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: 0.8643 (m-80) cc_final: 0.8298 (m-10) REVERT: T 76 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7994 (tptp) REVERT: T 88 ASP cc_start: 0.8045 (t0) cc_final: 0.7833 (t0) REVERT: R 29 MET cc_start: 0.8602 (mmm) cc_final: 0.8204 (mmm) REVERT: R 62 HIS cc_start: 0.8638 (t-90) cc_final: 0.8392 (t70) REVERT: R 63 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8435 (ttp80) REVERT: R 66 MET cc_start: 0.9044 (mmm) cc_final: 0.8835 (mmm) REVERT: Q 14 GLU cc_start: 0.9240 (tp30) cc_final: 0.9038 (tp30) REVERT: Q 32 ARG cc_start: 0.8851 (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: 0.8550 (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: 0.8598 (t0) cc_final: 0.8295 (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: 0.7214 (OUTLIER) cc_final: 0.6949 (tpp) REVERT: G 68 GLN cc_start: 0.7823 (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: 0.7164 (mtp) cc_final: 0.6800 (mtp) REVERT: G 134 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8152 (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: 0.7364 (tm-30) cc_final: 0.7126 (tm-30) REVERT: H 81 ASP cc_start: 0.8392 (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: 0.8878 (t0) cc_final: 0.8674 (t0) REVERT: K 496 PHE cc_start: 0.8451 (m-80) cc_final: 0.7924 (m-80) REVERT: K 500 GLU cc_start: 0.9128 (tt0) cc_final: 0.8842 (tp30) outliers start: 122 outliers final: 52 residues processed: 643 average time/residue: 1.2096 time to fit residues: 884.8416 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 : 2.165 ------------------------------------------------------------------------------- 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: 0.9990 chunk 138 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 62 optimal weight: 40.0000 chunk 210 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 68 GLN 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS T 79 HIS T 103 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS ** 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089999 restraints weight = 71090.738| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 5.48 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20223 Z= 0.157 Angle : 0.647 7.986 27351 Z= 0.327 Chirality : 0.044 0.202 2905 Planarity : 0.004 0.047 3638 Dihedral : 5.310 67.151 2730 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.35 % Allowed : 28.65 % Favored : 65.00 % 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: 1.94 (0.20), residues: 624 sheet: 0.13 (0.19), residues: 660 loop : 0.69 (0.22), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 509 HIS 0.014 0.001 HIS B 79 PHE 0.019 0.002 PHE S 131 TYR 0.023 0.002 TYR G 40 ARG 0.007 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 892) hydrogen bonds : angle 4.90373 ( 2490) covalent geometry : bond 0.00363 (20223) covalent geometry : angle 0.64707 (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 685 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 548 time to evaluate : 2.161 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 42 HIS cc_start: 0.8014 (t-90) cc_final: 0.7715 (t70) REVERT: A 81 ASP cc_start: 0.7391 (t0) cc_final: 0.7077 (t0) REVERT: A 88 ASP cc_start: 0.8260 (t0) cc_final: 0.7954 (t0) REVERT: A 117 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 63 ARG cc_start: 0.9343 (ptm160) cc_final: 0.9024 (ptm-80) REVERT: C 66 MET cc_start: 0.9183 (mmm) cc_final: 0.8969 (mmm) REVERT: C 81 ASP cc_start: 0.8203 (t0) cc_final: 0.7309 (t0) REVERT: D 28 ASP cc_start: 0.8395 (p0) cc_final: 0.8131 (p0) REVERT: D 29 MET cc_start: 0.9086 (mtm) cc_final: 0.8686 (pmm) REVERT: D 78 ARG cc_start: 0.8686 (tpm170) cc_final: 0.8188 (tpp-160) REVERT: D 81 ASP cc_start: 0.8401 (m-30) cc_final: 0.8162 (m-30) REVERT: D 90 VAL cc_start: 0.7497 (OUTLIER) cc_final: 0.7110 (p) REVERT: B 29 MET cc_start: 0.9060 (mpp) cc_final: 0.8805 (mpp) REVERT: B 59 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8602 (mmmt) REVERT: B 63 ARG cc_start: 0.9157 (tmm-80) cc_final: 0.8901 (tmm-80) REVERT: L 502 ASP cc_start: 0.7801 (m-30) cc_final: 0.7384 (t0) REVERT: I 495 ASP cc_start: 0.8485 (t0) cc_final: 0.8189 (t0) REVERT: I 496 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7638 (m-80) REVERT: P 88 ASP cc_start: 0.8199 (t0) cc_final: 0.7703 (t0) REVERT: P 123 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8161 (tptp) REVERT: N 1 MET cc_start: 0.7439 (tpp) cc_final: 0.6944 (tpp) REVERT: N 3 MET cc_start: 0.6972 (tpp) cc_final: 0.6705 (tpp) REVERT: N 29 MET cc_start: 0.8576 (tpp) cc_final: 0.7876 (mmm) REVERT: N 62 HIS cc_start: 0.8670 (t70) cc_final: 0.8287 (t-90) REVERT: N 117 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8171 (tm-30) REVERT: M 32 ARG cc_start: 0.8982 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: M 103 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: O 59 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8488 (mmmt) REVERT: O 103 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: U 479 ASN cc_start: 0.8491 (t0) cc_final: 0.8104 (t0) REVERT: U 496 PHE cc_start: 0.8681 (m-80) cc_final: 0.7908 (m-10) REVERT: T 88 ASP cc_start: 0.8134 (t0) cc_final: 0.7919 (t0) REVERT: R 29 MET cc_start: 0.8738 (mmm) cc_final: 0.8335 (mmm) REVERT: R 66 MET cc_start: 0.9084 (mmm) cc_final: 0.8872 (mmm) REVERT: Q 14 GLU cc_start: 0.9279 (tp30) cc_final: 0.8935 (tp30) REVERT: Q 93 GLN cc_start: 0.8645 (pp30) cc_final: 0.7818 (pp30) REVERT: Q 134 GLN cc_start: 0.8338 (tm-30) cc_final: 0.7953 (tm-30) REVERT: Q 136 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: W 479 ASN cc_start: 0.8622 (t0) cc_final: 0.8339 (t0) REVERT: W 480 ASP cc_start: 0.8807 (p0) cc_final: 0.8548 (p0) REVERT: W 496 PHE cc_start: 0.8560 (m-80) cc_final: 0.8355 (m-80) REVERT: E 59 LYS cc_start: 0.9121 (mmmm) cc_final: 0.8726 (mmmt) REVERT: E 76 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7957 (tptt) REVERT: G 25 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8248 (mm-40) REVERT: G 48 ASN cc_start: 0.9179 (t0) cc_final: 0.8885 (p0) REVERT: G 68 GLN cc_start: 0.7786 (mt0) cc_final: 0.7430 (mp10) REVERT: G 109 MET cc_start: 0.7929 (mtp) cc_final: 0.7562 (mtp) REVERT: G 134 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8277 (pt0) REVERT: H 32 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8689 (mmm-85) REVERT: H 60 GLU cc_start: 0.8962 (mp0) cc_final: 0.8621 (mp0) REVERT: H 68 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7262 (tm-30) REVERT: H 81 ASP cc_start: 0.8560 (m-30) cc_final: 0.7960 (m-30) REVERT: H 88 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8806 (t0) REVERT: K 495 ASP cc_start: 0.8936 (t0) cc_final: 0.8650 (t0) REVERT: K 496 PHE cc_start: 0.8629 (m-80) cc_final: 0.7971 (m-80) REVERT: K 500 GLU cc_start: 0.9130 (tt0) cc_final: 0.8779 (tp30) REVERT: K 503 ASP cc_start: 0.9446 (p0) cc_final: 0.8975 (p0) outliers start: 137 outliers final: 62 residues processed: 634 average time/residue: 1.2019 time to fit residues: 865.0318 Evaluate side-chains 582 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 511 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 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 75 THR Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain L residue 473 ILE 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 94 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 99 SER Chi-restraints excluded: chain M residue 10 LEU 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 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 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 486 LEU Chi-restraints excluded: chain U residue 487 SER 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 61 ILE 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 71 THR 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 S residue 114 LEU 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 76 LYS 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 H residue 88 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain K residue 473 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 143 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 217 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 74 HIS 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** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS T 68 GLN T 103 GLN R 24 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 48 ASN ** S 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS ** G 128 ASN ** 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 48 ASN F 58 GLN ** F 68 GLN ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.111101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085552 restraints weight = 71401.844| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 5.49 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20223 Z= 0.246 Angle : 0.701 10.539 27351 Z= 0.358 Chirality : 0.046 0.218 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.481 55.571 2722 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 6.86 % Allowed : 28.65 % Favored : 64.49 % 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: 1.01 (0.18), residues: 2415 helix: 1.91 (0.20), residues: 620 sheet: -0.00 (0.19), residues: 660 loop : 0.55 (0.21), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.010 0.001 HIS B 79 PHE 0.021 0.002 PHE S 131 TYR 0.013 0.002 TYR P 20 ARG 0.008 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 892) hydrogen bonds : angle 5.08397 ( 2490) covalent geometry : bond 0.00574 (20223) covalent geometry : angle 0.70069 (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 669 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 521 time to evaluate : 2.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7483 (t0) cc_final: 0.6975 (t0) REVERT: A 88 ASP cc_start: 0.8427 (t0) cc_final: 0.8137 (t0) REVERT: A 117 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8559 (mm-30) REVERT: C 63 ARG cc_start: 0.9394 (ptm160) cc_final: 0.9086 (ptm-80) REVERT: C 66 MET cc_start: 0.9180 (mmm) cc_final: 0.8962 (mmm) REVERT: D 17 ARG cc_start: 0.9031 (ppp80) cc_final: 0.8676 (ptm-80) REVERT: D 32 ARG cc_start: 0.8853 (mtm180) cc_final: 0.8584 (mtm180) REVERT: D 81 ASP cc_start: 0.8335 (m-30) cc_final: 0.8074 (m-30) REVERT: D 90 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7091 (p) REVERT: B 29 MET cc_start: 0.9012 (mpp) cc_final: 0.8726 (mpp) REVERT: B 59 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8627 (mmmt) REVERT: B 63 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8909 (tmm-80) REVERT: L 482 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: L 502 ASP cc_start: 0.7936 (m-30) cc_final: 0.7605 (p0) REVERT: I 479 ASN cc_start: 0.8851 (t0) cc_final: 0.8616 (t0) REVERT: I 495 ASP cc_start: 0.8624 (t70) cc_final: 0.8327 (t0) REVERT: P 88 ASP cc_start: 0.8443 (t0) cc_final: 0.8149 (t0) REVERT: N 1 MET cc_start: 0.7303 (tpp) cc_final: 0.6688 (tpp) REVERT: N 3 MET cc_start: 0.7328 (tpp) cc_final: 0.7051 (tpp) REVERT: N 62 HIS cc_start: 0.8696 (t70) cc_final: 0.8410 (t-90) REVERT: N 117 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8158 (tm-30) REVERT: M 17 ARG cc_start: 0.9023 (ppp80) cc_final: 0.8667 (ptm-80) REVERT: M 32 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: M 88 ASP cc_start: 0.9102 (m-30) cc_final: 0.8766 (t0) REVERT: M 103 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: O 59 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8592 (mmmt) REVERT: O 103 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: U 479 ASN cc_start: 0.8603 (t0) cc_final: 0.8188 (t0) REVERT: T 88 ASP cc_start: 0.8401 (t0) cc_final: 0.8149 (t0) REVERT: R 29 MET cc_start: 0.8799 (mmm) cc_final: 0.8537 (mmm) REVERT: R 63 ARG cc_start: 0.9273 (mtp-110) cc_final: 0.8968 (ttm-80) REVERT: R 107 ARG cc_start: 0.7059 (mmt90) cc_final: 0.6853 (mmt90) REVERT: Q 93 GLN cc_start: 0.8659 (pp30) cc_final: 0.7863 (pp30) REVERT: Q 101 ASN cc_start: 0.8730 (m-40) cc_final: 0.8504 (m110) REVERT: Q 103 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8089 (mp10) REVERT: Q 134 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8242 (tm-30) REVERT: Q 136 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: S 114 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7738 (mt) REVERT: W 479 ASN cc_start: 0.8660 (t0) cc_final: 0.8393 (t0) REVERT: E 59 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8719 (mmmt) REVERT: E 76 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8041 (tptt) REVERT: E 88 ASP cc_start: 0.8153 (t0) cc_final: 0.7902 (t0) REVERT: G 48 ASN cc_start: 0.9273 (t0) cc_final: 0.8958 (p0) REVERT: G 68 GLN cc_start: 0.7783 (mt0) cc_final: 0.7420 (mp10) REVERT: G 103 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8737 (mp10) REVERT: H 17 ARG cc_start: 0.8992 (ppp80) cc_final: 0.8613 (ptm-80) REVERT: H 60 GLU cc_start: 0.8973 (mp0) cc_final: 0.8600 (mp0) REVERT: H 68 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7545 (tm-30) REVERT: H 81 ASP cc_start: 0.8641 (m-30) cc_final: 0.8109 (m-30) REVERT: H 106 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (mtp180) REVERT: F 29 MET cc_start: 0.9053 (mpp) cc_final: 0.8771 (mpp) REVERT: F 53 ASP cc_start: 0.8955 (p0) cc_final: 0.8523 (p0) REVERT: F 103 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: J 482 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: K 495 ASP cc_start: 0.8937 (t0) cc_final: 0.8628 (t0) REVERT: K 496 PHE cc_start: 0.8927 (m-80) cc_final: 0.8517 (m-80) REVERT: K 500 GLU cc_start: 0.9287 (tt0) cc_final: 0.8637 (tp30) REVERT: K 503 ASP cc_start: 0.9299 (p0) cc_final: 0.8615 (p0) outliers start: 148 outliers final: 73 residues processed: 619 average time/residue: 1.1985 time to fit residues: 842.4014 Evaluate side-chains 580 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 494 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 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 86 LEU 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 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 P residue 41 VAL Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU 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 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 T residue 16 VAL Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 94 VAL 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 61 ILE Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 99 SER 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 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 S residue 114 LEU Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain X 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 76 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain G residue 2 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 205 optimal weight: 2.9990 chunk 75 optimal weight: 0.0170 chunk 19 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- 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 A 122 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** 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 74 HIS N 31 HIS 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** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN ** T 42 HIS ** 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 128 ASN ** S 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 HIS ** 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.112901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089268 restraints weight = 49053.371| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 4.55 r_work: 0.3295 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2951 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= 0.158 Angle : 0.690 10.216 27351 Z= 0.347 Chirality : 0.045 0.204 2905 Planarity : 0.004 0.052 3638 Dihedral : 5.265 55.917 2722 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.93 % Allowed : 29.72 % Favored : 64.35 % 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: 1.04 (0.18), residues: 2415 helix: 1.92 (0.20), residues: 624 sheet: -0.10 (0.18), residues: 720 loop : 0.71 (0.22), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 509 HIS 0.008 0.001 HIS B 79 PHE 0.018 0.002 PHE O 131 TYR 0.025 0.002 TYR R 40 ARG 0.009 0.001 ARG Q 63 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 892) hydrogen bonds : angle 4.97664 ( 2490) covalent geometry : bond 0.00371 (20223) covalent geometry : angle 0.69021 (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 673 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 545 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7702 (t0) cc_final: 0.7234 (t0) REVERT: A 88 ASP cc_start: 0.8461 (t0) cc_final: 0.8119 (t0) REVERT: A 123 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8588 (tptp) REVERT: A 132 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7515 (mtp85) REVERT: C 63 ARG cc_start: 0.9441 (ptm160) cc_final: 0.9101 (ptm-80) REVERT: C 66 MET cc_start: 0.9308 (mmm) cc_final: 0.9076 (mmm) REVERT: C 107 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7577 (mmt90) REVERT: D 17 ARG cc_start: 0.9123 (ppp80) cc_final: 0.8763 (ptm-80) REVERT: D 32 ARG cc_start: 0.8963 (mtm180) cc_final: 0.8519 (mtp180) REVERT: D 81 ASP cc_start: 0.8712 (m-30) cc_final: 0.8220 (m-30) REVERT: D 90 VAL cc_start: 0.7481 (OUTLIER) cc_final: 0.7048 (p) REVERT: D 93 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 107 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7839 (mtp85) REVERT: B 59 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8620 (mmmt) REVERT: B 63 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8962 (tmm-80) REVERT: L 482 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7907 (pm20) REVERT: L 502 ASP cc_start: 0.7943 (m-30) cc_final: 0.7625 (p0) REVERT: I 479 ASN cc_start: 0.8908 (t0) cc_final: 0.8667 (t0) REVERT: I 495 ASP cc_start: 0.8695 (t70) cc_final: 0.8399 (t0) REVERT: P 88 ASP cc_start: 0.8376 (t0) cc_final: 0.8080 (t0) REVERT: P 102 ASN cc_start: 0.9139 (t0) cc_final: 0.8752 (t0) REVERT: P 123 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8473 (tptm) REVERT: N 1 MET cc_start: 0.7372 (tpp) cc_final: 0.6805 (tpp) REVERT: N 3 MET cc_start: 0.7269 (tpp) cc_final: 0.6911 (tpp) REVERT: N 14 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7440 (tm-30) REVERT: N 29 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8552 (tpp) REVERT: N 62 HIS cc_start: 0.8713 (t70) cc_final: 0.8450 (t-90) REVERT: N 117 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8184 (tm-30) REVERT: M 17 ARG cc_start: 0.9080 (ppp80) cc_final: 0.8751 (ptm-80) REVERT: M 25 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8651 (mm-40) REVERT: M 32 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8710 (mmm-85) REVERT: M 68 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: M 103 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7298 (mp10) REVERT: M 117 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: M 123 LYS cc_start: 0.8767 (tppp) cc_final: 0.8530 (tptm) REVERT: O 59 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8596 (mmmt) REVERT: O 63 ARG cc_start: 0.9229 (ttt-90) cc_final: 0.8618 (ttp80) REVERT: O 103 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: U 479 ASN cc_start: 0.8684 (t0) cc_final: 0.8311 (t0) REVERT: U 491 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8006 (tm) REVERT: U 493 PHE cc_start: 0.8511 (m-80) cc_final: 0.8304 (m-80) REVERT: T 76 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7992 (tptt) REVERT: T 87 ASN cc_start: 0.9072 (m-40) cc_final: 0.8862 (m-40) REVERT: T 88 ASP cc_start: 0.8498 (t0) cc_final: 0.8225 (t0) REVERT: R 29 MET cc_start: 0.8785 (mmm) cc_final: 0.8466 (mmm) REVERT: R 63 ARG cc_start: 0.9332 (mtp-110) cc_final: 0.9117 (ttm-80) REVERT: Q 14 GLU cc_start: 0.9292 (tp30) cc_final: 0.8863 (tp30) REVERT: Q 93 GLN cc_start: 0.8749 (pp30) cc_final: 0.7991 (pp30) REVERT: Q 134 GLN cc_start: 0.8632 (tm-30) cc_final: 0.7957 (tm130) REVERT: Q 136 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: W 479 ASN cc_start: 0.8707 (t0) cc_final: 0.8427 (t0) REVERT: W 496 PHE cc_start: 0.8570 (m-80) cc_final: 0.8007 (m-10) REVERT: E 14 GLU cc_start: 0.8935 (tp30) cc_final: 0.8655 (tp30) REVERT: E 59 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8908 (mmtt) REVERT: E 88 ASP cc_start: 0.8186 (t0) cc_final: 0.7841 (t0) REVERT: G 3 MET cc_start: 0.7435 (mmm) cc_final: 0.7219 (tpp) REVERT: G 36 LYS cc_start: 0.9095 (tmmt) cc_final: 0.8860 (mmpt) REVERT: G 48 ASN cc_start: 0.9261 (t0) cc_final: 0.8954 (p0) REVERT: G 68 GLN cc_start: 0.7637 (mt0) cc_final: 0.7216 (mp10) REVERT: G 103 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8756 (mp10) REVERT: H 17 ARG cc_start: 0.9069 (ppp80) cc_final: 0.8712 (ptm-80) REVERT: H 60 GLU cc_start: 0.9205 (mp0) cc_final: 0.8880 (mp0) REVERT: H 68 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7749 (tm-30) REVERT: H 81 ASP cc_start: 0.8916 (m-30) cc_final: 0.8282 (m-30) REVERT: H 106 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: F 53 ASP cc_start: 0.9164 (p0) cc_final: 0.8752 (p0) REVERT: F 103 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: K 479 ASN cc_start: 0.9115 (t0) cc_final: 0.8821 (t0) REVERT: K 480 ASP cc_start: 0.9140 (t0) cc_final: 0.8878 (t0) REVERT: K 495 ASP cc_start: 0.8908 (t0) cc_final: 0.8562 (t0) REVERT: K 496 PHE cc_start: 0.8929 (m-80) cc_final: 0.8569 (m-80) REVERT: K 500 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8574 (tp30) REVERT: K 503 ASP cc_start: 0.9361 (p0) cc_final: 0.8728 (p0) outliers start: 128 outliers final: 63 residues processed: 632 average time/residue: 1.2206 time to fit residues: 874.7088 Evaluate side-chains 607 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 524 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 123 LYS 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 D residue 107 ARG Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 86 LEU 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 I residue 480 ASP Chi-restraints excluded: chain I residue 487 SER 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 29 MET 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 68 GLN Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain M residue 117 GLU 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 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 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 71 THR 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 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 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 86 LEU Chi-restraints excluded: chain H residue 106 ARG 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 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: 0.8980 chunk 122 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 215 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** 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 74 HIS N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** 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 83 HIS ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** 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 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 = 0.3824 r_free = 0.3824 target = 0.110852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086265 restraints weight = 68352.677| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 5.28 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20223 Z= 0.213 Angle : 0.714 11.509 27351 Z= 0.361 Chirality : 0.046 0.199 2905 Planarity : 0.004 0.053 3638 Dihedral : 5.341 56.514 2720 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 6.17 % Allowed : 31.02 % Favored : 62.82 % 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: 0.97 (0.18), residues: 2415 helix: 1.91 (0.20), residues: 618 sheet: -0.19 (0.18), residues: 728 loop : 0.71 (0.22), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP U 509 HIS 0.013 0.001 HIS F 79 PHE 0.020 0.002 PHE S 131 TYR 0.021 0.002 TYR C 40 ARG 0.012 0.001 ARG G 63 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 892) hydrogen bonds : angle 5.02979 ( 2490) covalent geometry : bond 0.00498 (20223) covalent geometry : angle 0.71404 (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 655 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 522 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7593 (t0) cc_final: 0.7018 (t0) REVERT: A 88 ASP cc_start: 0.8493 (t0) cc_final: 0.8174 (t0) REVERT: A 132 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7586 (mtp85) REVERT: C 58 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8919 (mm110) REVERT: C 63 ARG cc_start: 0.9385 (ptm160) cc_final: 0.9056 (ptm-80) REVERT: C 66 MET cc_start: 0.9168 (mmm) cc_final: 0.8930 (mmm) REVERT: D 32 ARG cc_start: 0.8830 (mtm180) cc_final: 0.8359 (mtp180) REVERT: D 63 ARG cc_start: 0.8586 (ttm110) cc_final: 0.8070 (ttm110) REVERT: D 81 ASP cc_start: 0.8341 (m-30) cc_final: 0.7550 (m-30) REVERT: D 90 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7089 (p) REVERT: D 93 GLN cc_start: 0.8840 (tm-30) cc_final: 0.7763 (tm-30) REVERT: B 29 MET cc_start: 0.9072 (mpp) cc_final: 0.8826 (mpp) REVERT: B 59 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8614 (mmmt) REVERT: B 63 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8856 (tmm-80) REVERT: L 482 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: L 502 ASP cc_start: 0.7903 (m-30) cc_final: 0.7567 (t0) REVERT: I 479 ASN cc_start: 0.8837 (t0) cc_final: 0.8526 (t0) REVERT: I 495 ASP cc_start: 0.8621 (t70) cc_final: 0.8349 (t0) REVERT: I 497 LEU cc_start: 0.9025 (mm) cc_final: 0.8664 (pp) REVERT: P 88 ASP cc_start: 0.8527 (t0) cc_final: 0.8052 (t0) REVERT: P 102 ASN cc_start: 0.8869 (t0) cc_final: 0.8420 (t0) REVERT: N 1 MET cc_start: 0.7308 (tpp) cc_final: 0.6986 (mmm) REVERT: N 3 MET cc_start: 0.7340 (tpp) cc_final: 0.6998 (tpp) REVERT: N 29 MET cc_start: 0.8998 (tpt) cc_final: 0.8590 (tpp) REVERT: N 62 HIS cc_start: 0.8686 (t70) cc_final: 0.8466 (t-90) REVERT: N 68 GLN cc_start: 0.7586 (mp10) cc_final: 0.7327 (mp10) REVERT: N 117 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8100 (tm-30) REVERT: M 25 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8573 (mm-40) REVERT: M 32 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8477 (mmm-85) REVERT: M 93 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8634 (tm-30) REVERT: M 117 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: M 123 LYS cc_start: 0.8790 (tppp) cc_final: 0.8537 (tptm) REVERT: O 59 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8562 (mmmt) REVERT: O 63 ARG cc_start: 0.9171 (ttt-90) cc_final: 0.8521 (ttp80) REVERT: O 103 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7080 (mp10) REVERT: V 502 ASP cc_start: 0.8307 (m-30) cc_final: 0.7455 (p0) REVERT: U 479 ASN cc_start: 0.8604 (t0) cc_final: 0.8270 (t0) REVERT: T 76 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7956 (tptt) REVERT: T 88 ASP cc_start: 0.8492 (t0) cc_final: 0.8211 (t0) REVERT: R 66 MET cc_start: 0.8936 (mmm) cc_final: 0.8727 (mmm) REVERT: Q 14 GLU cc_start: 0.9320 (tp30) cc_final: 0.8870 (tp30) REVERT: Q 63 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8114 (ttm110) REVERT: Q 93 GLN cc_start: 0.8643 (pp30) cc_final: 0.7944 (pp30) REVERT: Q 134 GLN cc_start: 0.8459 (tm-30) cc_final: 0.7903 (tm130) REVERT: S 63 ARG cc_start: 0.9191 (tmm-80) cc_final: 0.8952 (ttp80) REVERT: W 479 ASN cc_start: 0.8641 (t0) cc_final: 0.8359 (t0) REVERT: W 496 PHE cc_start: 0.8700 (m-80) cc_final: 0.8327 (m-10) REVERT: E 59 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8697 (mmmt) REVERT: E 76 LYS cc_start: 0.7843 (tptt) cc_final: 0.7060 (tptp) REVERT: E 88 ASP cc_start: 0.8400 (t0) cc_final: 0.8044 (t0) REVERT: G 36 LYS cc_start: 0.8983 (tmmt) cc_final: 0.8779 (mmpt) REVERT: G 48 ASN cc_start: 0.9271 (t0) cc_final: 0.8979 (p0) REVERT: G 103 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8739 (mp10) REVERT: H 17 ARG cc_start: 0.8977 (ppp80) cc_final: 0.8550 (ptm-80) REVERT: H 32 ARG cc_start: 0.9024 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: H 60 GLU cc_start: 0.8982 (mp0) cc_final: 0.8592 (mp0) REVERT: H 68 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7498 (tm-30) REVERT: H 81 ASP cc_start: 0.8651 (m-30) cc_final: 0.8069 (m-30) REVERT: H 106 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7917 (mtp180) REVERT: F 29 MET cc_start: 0.9071 (mpp) cc_final: 0.8837 (mpp) REVERT: F 39 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9107 (p) REVERT: F 53 ASP cc_start: 0.8943 (p0) cc_final: 0.8497 (p0) REVERT: F 101 ASN cc_start: 0.9163 (t0) cc_final: 0.8664 (t0) REVERT: F 103 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: J 482 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: K 479 ASN cc_start: 0.9058 (t0) cc_final: 0.8777 (t0) REVERT: K 480 ASP cc_start: 0.9139 (t0) cc_final: 0.8880 (t0) REVERT: K 495 ASP cc_start: 0.8857 (t0) cc_final: 0.8458 (t0) REVERT: K 500 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8382 (tm-30) outliers start: 133 outliers final: 75 residues processed: 612 average time/residue: 1.1995 time to fit residues: 832.5229 Evaluate side-chains 598 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 508 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 33 PHE 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 58 GLN 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 90 VAL Chi-restraints excluded: chain B residue 63 ARG 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 I residue 487 SER Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 55 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 117 GLU 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 479 ASN 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 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 71 THR Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 105 LEU 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 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 75 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 100 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 chunk 191 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** 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 P 74 HIS N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** 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 101 ASN S 102 ASN ** S 128 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 58 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.111691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087439 restraints weight = 60329.564| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 5.01 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20223 Z= 0.188 Angle : 0.732 10.263 27351 Z= 0.369 Chirality : 0.046 0.186 2905 Planarity : 0.004 0.054 3638 Dihedral : 5.263 57.088 2718 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 5.56 % Allowed : 32.41 % Favored : 62.03 % 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: 1.02 (0.18), residues: 2415 helix: 1.87 (0.20), residues: 618 sheet: -0.15 (0.18), residues: 720 loop : 0.77 (0.22), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.010 0.001 HIS F 79 PHE 0.019 0.002 PHE O 131 TYR 0.026 0.002 TYR R 40 ARG 0.011 0.001 ARG R 63 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 892) hydrogen bonds : angle 5.01386 ( 2490) covalent geometry : bond 0.00442 (20223) covalent geometry : angle 0.73202 (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 639 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 519 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7604 (t0) cc_final: 0.7064 (OUTLIER) REVERT: A 88 ASP cc_start: 0.8493 (t0) cc_final: 0.8180 (t0) REVERT: A 132 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7629 (mtp85) REVERT: C 58 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8919 (mm110) REVERT: C 63 ARG cc_start: 0.9382 (ptm160) cc_final: 0.9051 (ptm-80) REVERT: C 66 MET cc_start: 0.9161 (mmm) cc_final: 0.8939 (mmm) REVERT: D 17 ARG cc_start: 0.9008 (ppp80) cc_final: 0.8724 (ptm-80) REVERT: D 32 ARG cc_start: 0.8836 (mtm180) cc_final: 0.8330 (mtp180) REVERT: D 81 ASP cc_start: 0.8365 (m-30) cc_final: 0.8070 (m-30) REVERT: D 90 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7111 (p) REVERT: D 93 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8492 (tm130) REVERT: B 29 MET cc_start: 0.9074 (mpp) cc_final: 0.8782 (mpp) REVERT: B 59 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8609 (mmmt) REVERT: B 63 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8856 (tmm-80) REVERT: L 482 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: L 502 ASP cc_start: 0.7890 (m-30) cc_final: 0.7575 (t0) REVERT: I 479 ASN cc_start: 0.8844 (t0) cc_final: 0.8541 (t0) REVERT: I 495 ASP cc_start: 0.8719 (t70) cc_final: 0.8475 (t0) REVERT: I 497 LEU cc_start: 0.9058 (mm) cc_final: 0.8700 (pp) REVERT: P 29 MET cc_start: 0.8813 (mmp) cc_final: 0.8516 (mmp) REVERT: P 88 ASP cc_start: 0.8553 (t0) cc_final: 0.8054 (t0) REVERT: P 123 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8464 (tptm) REVERT: N 1 MET cc_start: 0.7321 (tpp) cc_final: 0.7008 (mmm) REVERT: N 3 MET cc_start: 0.7323 (tpp) cc_final: 0.6966 (tpp) REVERT: N 14 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7130 (tm-30) REVERT: N 29 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7921 (tpp) REVERT: N 32 ARG cc_start: 0.8863 (mmm-85) cc_final: 0.7983 (mtm-85) REVERT: N 62 HIS cc_start: 0.8714 (t70) cc_final: 0.8407 (t-90) REVERT: N 68 GLN cc_start: 0.7548 (mp10) cc_final: 0.7212 (mp10) REVERT: N 107 ARG cc_start: 0.7574 (mmt90) cc_final: 0.7310 (mmt90) REVERT: N 117 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8128 (tm-30) REVERT: M 17 ARG cc_start: 0.9017 (ppp80) cc_final: 0.8798 (ppp80) REVERT: M 25 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8569 (mm-40) REVERT: M 32 ARG cc_start: 0.8985 (mmm-85) cc_final: 0.8485 (mmm-85) REVERT: M 93 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8219 (tm-30) REVERT: O 59 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8556 (mmmt) REVERT: O 63 ARG cc_start: 0.9148 (ttt-90) cc_final: 0.8517 (ttp80) REVERT: O 103 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: V 502 ASP cc_start: 0.8311 (m-30) cc_final: 0.7546 (p0) REVERT: U 479 ASN cc_start: 0.8629 (t0) cc_final: 0.8295 (t0) REVERT: T 76 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8040 (tptp) REVERT: T 88 ASP cc_start: 0.8477 (t0) cc_final: 0.8199 (t0) REVERT: R 63 ARG cc_start: 0.9271 (mtp-110) cc_final: 0.8859 (tpm170) REVERT: R 107 ARG cc_start: 0.7167 (mmt90) cc_final: 0.6706 (mmt90) REVERT: Q 14 GLU cc_start: 0.9319 (tp30) cc_final: 0.8861 (tp30) REVERT: Q 63 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8102 (ttm110) REVERT: Q 93 GLN cc_start: 0.8667 (pp30) cc_final: 0.7930 (pp30) REVERT: Q 134 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8175 (tm-30) REVERT: Q 136 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8633 (pp20) REVERT: W 479 ASN cc_start: 0.8637 (t0) cc_final: 0.8362 (t0) REVERT: W 496 PHE cc_start: 0.8781 (m-80) cc_final: 0.8447 (m-10) REVERT: E 59 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8706 (mmmt) REVERT: E 88 ASP cc_start: 0.8425 (t0) cc_final: 0.8053 (t0) REVERT: G 48 ASN cc_start: 0.9261 (t0) cc_final: 0.8947 (p0) REVERT: G 103 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: H 17 ARG cc_start: 0.8994 (ppp80) cc_final: 0.8787 (ppp80) REVERT: H 60 GLU cc_start: 0.8984 (mp0) cc_final: 0.8691 (mp0) REVERT: H 68 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7534 (tm-30) REVERT: H 81 ASP cc_start: 0.8647 (m-30) cc_final: 0.8161 (m-30) REVERT: H 106 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (mtp180) REVERT: F 29 MET cc_start: 0.9091 (mpp) cc_final: 0.8825 (mpp) REVERT: F 53 ASP cc_start: 0.8955 (p0) cc_final: 0.8508 (p0) REVERT: F 103 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7402 (mp10) REVERT: J 495 ASP cc_start: 0.8158 (m-30) cc_final: 0.7828 (p0) REVERT: K 479 ASN cc_start: 0.9059 (t0) cc_final: 0.8776 (t0) REVERT: K 480 ASP cc_start: 0.9119 (t0) cc_final: 0.8880 (t0) REVERT: K 495 ASP cc_start: 0.8881 (t0) cc_final: 0.8506 (t0) REVERT: K 496 PHE cc_start: 0.8944 (m-80) cc_final: 0.8742 (m-80) REVERT: K 500 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8547 (tp30) outliers start: 120 outliers final: 80 residues processed: 603 average time/residue: 1.2275 time to fit residues: 839.0590 Evaluate side-chains 601 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 507 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 58 GLN Chi-restraints excluded: chain C residue 61 ILE 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 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 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 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 480 ASP Chi-restraints excluded: chain I residue 487 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 94 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 29 MET Chi-restraints excluded: chain N residue 55 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 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 479 ASN Chi-restraints excluded: chain V residue 483 ILE Chi-restraints excluded: chain V residue 492 THR 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 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 77 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN 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 S residue 114 LEU Chi-restraints excluded: chain S residue 117 GLU 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 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 75 THR 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 42 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 22 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 214 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN P 68 GLN P 74 HIS 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** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 58 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.112522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087762 restraints weight = 72726.768| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 5.45 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20223 Z= 0.169 Angle : 0.750 12.199 27351 Z= 0.374 Chirality : 0.046 0.197 2905 Planarity : 0.004 0.052 3638 Dihedral : 5.230 57.717 2718 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.38 % Allowed : 32.68 % Favored : 61.94 % 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: 1.04 (0.18), residues: 2415 helix: 1.84 (0.21), residues: 618 sheet: -0.15 (0.18), residues: 724 loop : 0.83 (0.22), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.023 0.001 HIS H 42 PHE 0.018 0.002 PHE O 131 TYR 0.023 0.002 TYR C 40 ARG 0.010 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 892) hydrogen bonds : angle 5.01953 ( 2490) covalent geometry : bond 0.00400 (20223) covalent geometry : angle 0.75025 (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 653 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 537 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7595 (t0) cc_final: 0.7017 (t0) REVERT: A 88 ASP cc_start: 0.8516 (t0) cc_final: 0.8164 (t0) REVERT: A 132 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7560 (mtp85) REVERT: C 32 ARG cc_start: 0.8838 (ttp80) cc_final: 0.8114 (ttp80) REVERT: C 58 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8897 (mm110) REVERT: C 63 ARG cc_start: 0.9401 (ptm160) cc_final: 0.9053 (ptm-80) REVERT: D 17 ARG cc_start: 0.8974 (ppp80) cc_final: 0.8642 (ptm-80) REVERT: D 32 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8337 (mtp180) REVERT: D 78 ARG cc_start: 0.8591 (tpt170) cc_final: 0.8378 (ttm-80) REVERT: D 81 ASP cc_start: 0.8308 (m-30) cc_final: 0.7901 (m-30) REVERT: D 90 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7063 (p) REVERT: D 93 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8150 (tm130) REVERT: D 135 ASP cc_start: 0.8455 (m-30) cc_final: 0.8001 (m-30) REVERT: B 29 MET cc_start: 0.9073 (mpp) cc_final: 0.8873 (mpp) REVERT: B 59 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8621 (mmmt) REVERT: B 63 ARG cc_start: 0.9151 (OUTLIER) cc_final: 0.8844 (tmm-80) REVERT: B 101 ASN cc_start: 0.9338 (t0) cc_final: 0.9017 (t0) REVERT: L 477 ASP cc_start: 0.8951 (p0) cc_final: 0.8654 (p0) REVERT: L 482 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: L 486 LEU cc_start: 0.8484 (tp) cc_final: 0.8166 (mp) REVERT: L 502 ASP cc_start: 0.7894 (m-30) cc_final: 0.7578 (t0) REVERT: I 479 ASN cc_start: 0.8907 (t0) cc_final: 0.8051 (t0) REVERT: I 480 ASP cc_start: 0.8867 (t0) cc_final: 0.8080 (p0) REVERT: I 495 ASP cc_start: 0.8710 (t70) cc_final: 0.8498 (t0) REVERT: I 497 LEU cc_start: 0.9003 (mm) cc_final: 0.8640 (pp) REVERT: P 29 MET cc_start: 0.8802 (mmp) cc_final: 0.8517 (mmp) REVERT: P 88 ASP cc_start: 0.8540 (t0) cc_final: 0.8029 (t0) REVERT: P 123 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8407 (tptm) REVERT: P 132 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7731 (mtp85) REVERT: N 1 MET cc_start: 0.7398 (tpp) cc_final: 0.7079 (mmm) REVERT: N 3 MET cc_start: 0.7203 (tpp) cc_final: 0.6842 (tpp) REVERT: N 29 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.7861 (tpp) REVERT: N 32 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.7921 (mtm-85) REVERT: N 62 HIS cc_start: 0.8680 (t70) cc_final: 0.8329 (t-90) REVERT: N 107 ARG cc_start: 0.7520 (mmt90) cc_final: 0.7232 (mmt90) REVERT: N 117 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8105 (tm-30) REVERT: M 17 ARG cc_start: 0.9017 (ppp80) cc_final: 0.8756 (ppp80) REVERT: M 25 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8584 (mm-40) REVERT: M 32 ARG cc_start: 0.8980 (mmm-85) cc_final: 0.8612 (mmm-85) REVERT: M 93 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8180 (tm-30) REVERT: M 103 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8061 (mp10) REVERT: O 59 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8554 (mmmt) REVERT: O 63 ARG cc_start: 0.9145 (ttt-90) cc_final: 0.8526 (ttp80) REVERT: O 103 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: V 502 ASP cc_start: 0.8370 (m-30) cc_final: 0.7577 (p0) REVERT: U 479 ASN cc_start: 0.8649 (t0) cc_final: 0.8314 (t0) REVERT: U 500 GLU cc_start: 0.9220 (tt0) cc_final: 0.8906 (tt0) REVERT: T 76 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7962 (tptt) REVERT: T 88 ASP cc_start: 0.8437 (t0) cc_final: 0.8158 (t0) REVERT: R 63 ARG cc_start: 0.9275 (mtp-110) cc_final: 0.8973 (ttm-80) REVERT: Q 14 GLU cc_start: 0.9321 (tp30) cc_final: 0.8862 (tp30) REVERT: Q 32 ARG cc_start: 0.9032 (mmm-85) cc_final: 0.8696 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8690 (pp30) cc_final: 0.7828 (pp30) REVERT: Q 109 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7996 (ttt) REVERT: Q 134 GLN cc_start: 0.8455 (tm-30) cc_final: 0.7935 (tm130) REVERT: Q 136 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8660 (pp20) REVERT: W 479 ASN cc_start: 0.8623 (t0) cc_final: 0.8336 (t0) REVERT: E 59 LYS cc_start: 0.9115 (mmmm) cc_final: 0.8698 (mmmt) REVERT: E 88 ASP cc_start: 0.8493 (t0) cc_final: 0.8101 (t0) REVERT: E 102 ASN cc_start: 0.8849 (t0) cc_final: 0.8434 (t0) REVERT: E 109 MET cc_start: 0.8912 (ptm) cc_final: 0.8707 (ptp) REVERT: G 34 TYR cc_start: 0.8423 (m-80) cc_final: 0.8147 (m-80) REVERT: G 48 ASN cc_start: 0.9269 (t0) cc_final: 0.8953 (p0) REVERT: G 103 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8739 (mp10) REVERT: H 17 ARG cc_start: 0.8999 (ppp80) cc_final: 0.8588 (ppp80) REVERT: H 32 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8597 (mmm-85) REVERT: H 60 GLU cc_start: 0.9003 (mp0) cc_final: 0.8669 (mp0) REVERT: H 68 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7507 (tm-30) REVERT: H 81 ASP cc_start: 0.8635 (m-30) cc_final: 0.8161 (m-30) REVERT: H 106 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7905 (mtp180) REVERT: F 29 MET cc_start: 0.9072 (mpp) cc_final: 0.8794 (mpp) REVERT: F 53 ASP cc_start: 0.8968 (p0) cc_final: 0.8548 (p0) REVERT: F 103 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: J 495 ASP cc_start: 0.8123 (m-30) cc_final: 0.7844 (p0) REVERT: K 479 ASN cc_start: 0.9072 (t0) cc_final: 0.8776 (t0) REVERT: K 480 ASP cc_start: 0.9126 (t0) cc_final: 0.8883 (t0) REVERT: K 495 ASP cc_start: 0.8834 (t0) cc_final: 0.8442 (t0) REVERT: K 496 PHE cc_start: 0.8978 (m-80) cc_final: 0.8762 (m-80) REVERT: K 500 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8507 (tp30) outliers start: 116 outliers final: 75 residues processed: 619 average time/residue: 1.2092 time to fit residues: 849.6710 Evaluate side-chains 608 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 515 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 58 GLN Chi-restraints excluded: chain C residue 61 ILE 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 29 MET 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 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 504 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 94 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 29 MET Chi-restraints excluded: chain N residue 55 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 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 V residue 483 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 474 THR 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 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 77 ILE Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 105 LEU 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 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 S residue 137 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 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 HIS 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 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 J residue 506 ASP 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: 8.9990 chunk 132 optimal weight: 6.9990 chunk 223 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 103 GLN C 93 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN N 37 ASN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS T 68 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** 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 ** 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 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.112654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.088349 restraints weight = 63603.921| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 5.14 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20223 Z= 0.174 Angle : 0.779 12.289 27351 Z= 0.387 Chirality : 0.046 0.211 2905 Planarity : 0.004 0.052 3638 Dihedral : 5.241 58.930 2718 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.96 % Allowed : 33.66 % Favored : 61.38 % 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: 1.01 (0.18), residues: 2415 helix: 1.79 (0.21), residues: 618 sheet: -0.19 (0.18), residues: 724 loop : 0.85 (0.22), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.027 0.001 HIS H 42 PHE 0.019 0.002 PHE B 131 TYR 0.030 0.002 TYR R 40 ARG 0.011 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 892) hydrogen bonds : angle 5.01838 ( 2490) covalent geometry : bond 0.00412 (20223) covalent geometry : angle 0.77863 (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 640 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 533 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9104 (m-30) cc_final: 0.8614 (p0) REVERT: A 81 ASP cc_start: 0.7640 (t0) cc_final: 0.7081 (t0) REVERT: A 88 ASP cc_start: 0.8537 (t0) cc_final: 0.8219 (t0) REVERT: A 123 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8705 (tptp) REVERT: A 132 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7624 (mtp85) REVERT: C 36 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8608 (mmpt) REVERT: C 58 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8436 (mm110) REVERT: C 63 ARG cc_start: 0.9374 (ptm160) cc_final: 0.9037 (ptm-80) REVERT: D 17 ARG cc_start: 0.8980 (ppp80) cc_final: 0.8620 (ptm-80) REVERT: D 32 ARG cc_start: 0.8810 (mtm180) cc_final: 0.8286 (mtp180) REVERT: D 81 ASP cc_start: 0.8304 (m-30) cc_final: 0.7942 (m-30) REVERT: D 90 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7019 (p) REVERT: D 93 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8175 (tm130) REVERT: D 135 ASP cc_start: 0.8421 (m-30) cc_final: 0.8018 (m-30) REVERT: B 29 MET cc_start: 0.9101 (mpp) cc_final: 0.8890 (mpp) REVERT: B 59 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8612 (mmmt) REVERT: B 63 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8838 (tmm-80) REVERT: L 482 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8055 (pt0) REVERT: L 486 LEU cc_start: 0.8483 (tp) cc_final: 0.8154 (mp) REVERT: L 502 ASP cc_start: 0.7879 (m-30) cc_final: 0.7596 (t0) REVERT: I 479 ASN cc_start: 0.8851 (t0) cc_final: 0.8046 (t0) REVERT: I 480 ASP cc_start: 0.8828 (t0) cc_final: 0.7931 (p0) REVERT: I 495 ASP cc_start: 0.8719 (t70) cc_final: 0.8400 (t0) REVERT: P 88 ASP cc_start: 0.8560 (t0) cc_final: 0.8030 (t0) REVERT: P 102 ASN cc_start: 0.8788 (t0) cc_final: 0.8508 (t0) REVERT: P 123 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8403 (tptm) REVERT: P 132 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7782 (mtp85) REVERT: N 1 MET cc_start: 0.7400 (tpp) cc_final: 0.7079 (mmm) REVERT: N 3 MET cc_start: 0.7235 (tpp) cc_final: 0.6865 (tpp) REVERT: N 29 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8571 (tpp) REVERT: N 36 LYS cc_start: 0.8756 (tmmt) cc_final: 0.8325 (mmpt) REVERT: N 37 ASN cc_start: 0.8312 (OUTLIER) cc_final: 0.7664 (t0) REVERT: N 62 HIS cc_start: 0.8632 (t70) cc_final: 0.8342 (t-90) REVERT: N 117 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8119 (tm-30) REVERT: M 17 ARG cc_start: 0.9002 (ppp80) cc_final: 0.8768 (ppp80) REVERT: M 25 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8620 (mm-40) REVERT: M 32 ARG cc_start: 0.9008 (mmm-85) cc_final: 0.8617 (mmm-85) REVERT: M 66 MET cc_start: 0.8955 (mmp) cc_final: 0.8678 (mmm) REVERT: M 93 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8060 (tm-30) REVERT: M 103 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: O 59 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8554 (mmmt) REVERT: O 63 ARG cc_start: 0.9131 (ttt-90) cc_final: 0.8509 (ttp80) REVERT: O 103 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: V 502 ASP cc_start: 0.8406 (m-30) cc_final: 0.7569 (p0) REVERT: U 479 ASN cc_start: 0.8628 (t0) cc_final: 0.8304 (t0) REVERT: U 500 GLU cc_start: 0.9255 (tt0) cc_final: 0.8939 (tt0) REVERT: T 76 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8140 (tptp) REVERT: T 88 ASP cc_start: 0.8441 (t0) cc_final: 0.8156 (t0) REVERT: R 36 LYS cc_start: 0.8909 (tmmt) cc_final: 0.8634 (mmpt) REVERT: R 63 ARG cc_start: 0.9267 (mtp-110) cc_final: 0.9063 (ttm-80) REVERT: R 103 GLN cc_start: 0.8422 (mp10) cc_final: 0.8211 (mp10) REVERT: Q 14 GLU cc_start: 0.9319 (tp30) cc_final: 0.8777 (tp30) REVERT: Q 32 ARG cc_start: 0.9036 (mmm-85) cc_final: 0.8668 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8683 (pp30) cc_final: 0.7907 (pp30) REVERT: Q 134 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8100 (tm-30) REVERT: Q 136 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8637 (pp20) REVERT: W 479 ASN cc_start: 0.8601 (t0) cc_final: 0.8315 (t0) REVERT: E 14 GLU cc_start: 0.8676 (tp30) cc_final: 0.8459 (tp30) REVERT: E 59 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8713 (mmmt) REVERT: E 88 ASP cc_start: 0.8530 (t0) cc_final: 0.8153 (t0) REVERT: E 102 ASN cc_start: 0.8848 (t0) cc_final: 0.8434 (t0) REVERT: G 48 ASN cc_start: 0.9254 (t0) cc_final: 0.8947 (p0) REVERT: G 103 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8770 (mp10) REVERT: H 17 ARG cc_start: 0.8983 (ppp80) cc_final: 0.8588 (ppp80) REVERT: H 59 LYS cc_start: 0.9115 (tptt) cc_final: 0.8907 (tptt) REVERT: H 60 GLU cc_start: 0.8975 (mp0) cc_final: 0.8636 (mp0) REVERT: H 68 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7497 (tm-30) REVERT: H 81 ASP cc_start: 0.8617 (m-30) cc_final: 0.8204 (m-30) REVERT: H 106 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7922 (mtp180) REVERT: F 29 MET cc_start: 0.9069 (mpp) cc_final: 0.8785 (mpp) REVERT: F 53 ASP cc_start: 0.8931 (p0) cc_final: 0.8514 (p0) REVERT: F 103 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: J 495 ASP cc_start: 0.8157 (m-30) cc_final: 0.7910 (p0) REVERT: K 479 ASN cc_start: 0.9049 (t0) cc_final: 0.8750 (t0) REVERT: K 480 ASP cc_start: 0.9110 (t0) cc_final: 0.8873 (t0) REVERT: K 495 ASP cc_start: 0.8838 (t0) cc_final: 0.8463 (t0) REVERT: K 496 PHE cc_start: 0.9047 (m-80) cc_final: 0.8841 (m-80) REVERT: K 500 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8415 (tp30) outliers start: 107 outliers final: 72 residues processed: 606 average time/residue: 1.2436 time to fit residues: 852.8518 Evaluate side-chains 607 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 517 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 58 GLN Chi-restraints excluded: chain C residue 61 ILE 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 30 LEU 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 482 GLU Chi-restraints excluded: chain L residue 492 THR Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 487 SER Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 94 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 29 MET Chi-restraints excluded: chain N residue 37 ASN 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 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 V residue 483 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 474 THR 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 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 114 LEU 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 90 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN 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 S residue 114 LEU Chi-restraints excluded: chain S residue 117 GLU Chi-restraints excluded: chain S residue 137 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 42 HIS 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 75 THR 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 486 LEU 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: 4.9990 chunk 68 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 120 optimal weight: 0.0570 chunk 182 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 197 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 42 HIS ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.112870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.088668 restraints weight = 60226.698| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 5.02 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3429 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= 0.174 Angle : 0.788 13.074 27351 Z= 0.391 Chirality : 0.046 0.202 2905 Planarity : 0.004 0.053 3638 Dihedral : 5.250 59.664 2716 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.54 % Allowed : 33.98 % Favored : 61.47 % 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: 0.99 (0.18), residues: 2415 helix: 1.73 (0.21), residues: 618 sheet: -0.19 (0.18), residues: 724 loop : 0.85 (0.22), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 509 HIS 0.015 0.001 HIS F 79 PHE 0.018 0.002 PHE B 131 TYR 0.023 0.002 TYR C 40 ARG 0.012 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 892) hydrogen bonds : angle 5.05493 ( 2490) covalent geometry : bond 0.00409 (20223) covalent geometry : angle 0.78786 (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 623 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 525 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9099 (m-30) cc_final: 0.8608 (p0) REVERT: A 81 ASP cc_start: 0.7663 (t0) cc_final: 0.7087 (t0) REVERT: A 88 ASP cc_start: 0.8523 (t0) cc_final: 0.8206 (t0) REVERT: A 123 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: A 132 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7458 (mtp85) REVERT: C 32 ARG cc_start: 0.8837 (ttp80) cc_final: 0.8146 (ttp80) REVERT: C 36 LYS cc_start: 0.8978 (tmmt) cc_final: 0.8603 (mmpt) REVERT: C 58 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8408 (mm110) REVERT: C 63 ARG cc_start: 0.9399 (ptm160) cc_final: 0.9060 (ptm-80) REVERT: D 17 ARG cc_start: 0.8966 (ppp80) cc_final: 0.8596 (ptm-80) REVERT: D 32 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8295 (mtp180) REVERT: D 81 ASP cc_start: 0.8325 (m-30) cc_final: 0.7947 (m-30) REVERT: D 90 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.6988 (p) REVERT: D 93 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8229 (tm130) REVERT: D 135 ASP cc_start: 0.8388 (m-30) cc_final: 0.7958 (m-30) REVERT: B 29 MET cc_start: 0.9111 (mpp) cc_final: 0.8899 (mpp) REVERT: B 59 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8602 (mmmt) REVERT: B 101 ASN cc_start: 0.9303 (t0) cc_final: 0.8591 (t0) REVERT: L 482 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: L 486 LEU cc_start: 0.8488 (tp) cc_final: 0.8183 (mp) REVERT: L 502 ASP cc_start: 0.7872 (m-30) cc_final: 0.7591 (t0) REVERT: I 479 ASN cc_start: 0.8860 (t0) cc_final: 0.8080 (t0) REVERT: I 480 ASP cc_start: 0.8837 (t0) cc_final: 0.7980 (p0) REVERT: I 495 ASP cc_start: 0.8701 (t70) cc_final: 0.8438 (t0) REVERT: P 88 ASP cc_start: 0.8477 (t0) cc_final: 0.7996 (t0) REVERT: P 102 ASN cc_start: 0.8801 (t0) cc_final: 0.8503 (t0) REVERT: P 123 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8381 (tptm) REVERT: P 132 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7776 (mtp85) REVERT: N 1 MET cc_start: 0.7351 (tpp) cc_final: 0.7032 (mmm) REVERT: N 3 MET cc_start: 0.7202 (tpp) cc_final: 0.6826 (tpp) REVERT: N 29 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8693 (ttm) REVERT: N 62 HIS cc_start: 0.8584 (t70) cc_final: 0.8377 (t-90) REVERT: N 68 GLN cc_start: 0.7650 (mp10) cc_final: 0.7084 (mp10) REVERT: N 109 MET cc_start: 0.8640 (ttm) cc_final: 0.8225 (ttm) REVERT: N 117 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8134 (tm-30) REVERT: N 123 LYS cc_start: 0.8403 (ttpt) cc_final: 0.8131 (tppp) REVERT: M 17 ARG cc_start: 0.9024 (ppp80) cc_final: 0.8769 (ppp80) REVERT: M 25 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8603 (mm-40) REVERT: M 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8592 (mmm-85) REVERT: M 66 MET cc_start: 0.8981 (mmp) cc_final: 0.8726 (mmm) REVERT: M 93 GLN cc_start: 0.8525 (tm-30) cc_final: 0.7960 (tm-30) REVERT: M 103 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8045 (mp10) REVERT: O 59 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8551 (mmmt) REVERT: O 63 ARG cc_start: 0.9089 (ttt-90) cc_final: 0.8469 (ttp80) REVERT: O 103 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: V 502 ASP cc_start: 0.8350 (m-30) cc_final: 0.7556 (p0) REVERT: U 479 ASN cc_start: 0.8612 (t0) cc_final: 0.8289 (t0) REVERT: U 500 GLU cc_start: 0.9269 (tt0) cc_final: 0.8920 (tt0) REVERT: T 76 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8022 (tptp) REVERT: T 88 ASP cc_start: 0.8458 (t0) cc_final: 0.8175 (t0) REVERT: R 29 MET cc_start: 0.9012 (mtp) cc_final: 0.8578 (tpt) REVERT: R 36 LYS cc_start: 0.8901 (tmmt) cc_final: 0.8612 (mmpt) REVERT: R 63 ARG cc_start: 0.9274 (mtp-110) cc_final: 0.8890 (ptm160) REVERT: R 103 GLN cc_start: 0.8440 (mp10) cc_final: 0.8235 (mp10) REVERT: Q 14 GLU cc_start: 0.9308 (tp30) cc_final: 0.8821 (tp30) REVERT: Q 32 ARG cc_start: 0.9025 (mmm-85) cc_final: 0.8670 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8684 (pp30) cc_final: 0.7918 (pp30) REVERT: Q 133 TYR cc_start: 0.8819 (m-80) cc_final: 0.8530 (m-80) REVERT: Q 134 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8181 (tm-30) REVERT: Q 136 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8642 (pp20) REVERT: W 479 ASN cc_start: 0.8615 (t0) cc_final: 0.8322 (t0) REVERT: E 59 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8709 (mmmt) REVERT: E 88 ASP cc_start: 0.8533 (t0) cc_final: 0.8154 (t0) REVERT: E 102 ASN cc_start: 0.8848 (t0) cc_final: 0.8430 (t0) REVERT: G 48 ASN cc_start: 0.9255 (t0) cc_final: 0.8993 (p0) REVERT: G 63 ARG cc_start: 0.9192 (ttm-80) cc_final: 0.8869 (tpp-160) REVERT: G 103 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: H 17 ARG cc_start: 0.8973 (ppp80) cc_final: 0.8575 (ppp80) REVERT: H 60 GLU cc_start: 0.8998 (mp0) cc_final: 0.8696 (mp0) REVERT: H 68 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7501 (tm-30) REVERT: H 81 ASP cc_start: 0.8609 (m-30) cc_final: 0.8199 (m-30) REVERT: H 106 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7925 (mtp180) REVERT: F 29 MET cc_start: 0.9083 (mpp) cc_final: 0.8796 (mpp) REVERT: F 53 ASP cc_start: 0.8923 (p0) cc_final: 0.8507 (p0) REVERT: F 103 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: J 495 ASP cc_start: 0.8139 (m-30) cc_final: 0.7895 (p0) REVERT: K 479 ASN cc_start: 0.9060 (t0) cc_final: 0.8757 (t0) REVERT: K 480 ASP cc_start: 0.9114 (t0) cc_final: 0.8887 (t0) REVERT: K 495 ASP cc_start: 0.8813 (t0) cc_final: 0.8420 (t0) REVERT: K 496 PHE cc_start: 0.9037 (m-80) cc_final: 0.8823 (m-80) REVERT: K 500 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8436 (tp30) outliers start: 98 outliers final: 68 residues processed: 591 average time/residue: 1.2554 time to fit residues: 839.8858 Evaluate side-chains 596 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 511 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 90 VAL 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 482 GLU Chi-restraints excluded: chain L residue 492 THR 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 94 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 29 MET 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 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 483 ILE Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 474 THR 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 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 114 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 90 VAL 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 117 GLU Chi-restraints excluded: chain S residue 137 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 73 CYS Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 42 HIS 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 75 THR 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 486 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 1 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 193 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS Q 101 ASN S 62 HIS ** S 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS H 69 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.114286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.090071 restraints weight = 65830.330| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 5.20 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3481 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3481 r_free = 0.3481 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3481 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3540 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= 0.151 Angle : 0.792 12.898 27351 Z= 0.392 Chirality : 0.046 0.205 2905 Planarity : 0.004 0.057 3638 Dihedral : 5.196 59.550 2716 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.17 % Allowed : 34.26 % Favored : 61.57 % 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: 0.95 (0.18), residues: 2415 helix: 1.69 (0.21), residues: 618 sheet: -0.23 (0.18), residues: 736 loop : 0.88 (0.23), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP U 509 HIS 0.014 0.001 HIS F 79 PHE 0.016 0.002 PHE O 131 TYR 0.030 0.002 TYR R 40 ARG 0.011 0.001 ARG N 63 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 892) hydrogen bonds : angle 5.03767 ( 2490) covalent geometry : bond 0.00356 (20223) covalent geometry : angle 0.79224 (27351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16371.09 seconds wall clock time: 279 minutes 46.91 seconds (16786.91 seconds total)