Starting phenix.real_space_refine on Thu Sep 18 19:29:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ivs_60934/09_2025/9ivs_60934.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ivs_60934/09_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_60934/09_2025/9ivs_60934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ivs_60934/09_2025/9ivs_60934.map" model { file = "/net/cci-nas-00/data/ceres_data/9ivs_60934/09_2025/9ivs_60934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ivs_60934/09_2025/9ivs_60934.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19758 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "C" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "D" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "B" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "L" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 282 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "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: 5.02, per 1000 atoms: 0.25 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: 1.71 Conformation dependent library (CDL) restraints added in 829.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4830 Ramachandran restraints generated. 2415 Oldfield, 0 Emsley, 2415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4570 Finding SS restraints... Secondary structure from input PDB file: 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: 0.68 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: 3.40 Time building geometry restraints manager: 2.30 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.960 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.720 ------------------------------------------------------------------------------- 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 : 18.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (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 ARG 0.010 0.001 ARG M 63 TYR 0.025 0.002 TYR S 125 PHE 0.032 0.002 PHE K 493 TRP 0.005 0.001 TRP U 509 HIS 0.013 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00647 (20223) covalent geometry : angle 0.95535 (27351) hydrogen bonds : bond 0.11894 ( 892) hydrogen bonds : angle 6.08173 ( 2490) *********************** 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 : 0.842 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: 0.8937 (mtm) REVERT: D 32 ARG cc_start: 0.9058 (mtp85) cc_final: 0.8808 (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: 0.5738 time to fit residues: 415.7652 Evaluate side-chains 553 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 510 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 128 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** 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 ** 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.118095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.092577 restraints weight = 73456.340| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 5.68 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20223 Z= 0.137 Angle : 0.652 10.875 27351 Z= 0.331 Chirality : 0.044 0.172 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.839 73.835 2767 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 5.84 % Allowed : 28.33 % Favored : 65.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2415 helix: 1.84 (0.20), residues: 620 sheet: 0.03 (0.19), residues: 684 loop : 0.57 (0.22), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 63 TYR 0.018 0.002 TYR N 20 PHE 0.018 0.002 PHE A 15 TRP 0.005 0.001 TRP K 509 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00315 (20223) covalent geometry : angle 0.65169 (27351) hydrogen bonds : bond 0.03540 ( 892) hydrogen bonds : angle 5.05418 ( 2490) *********************** 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 700 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 574 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7343 (t0) cc_final: 0.7130 (t0) REVERT: A 88 ASP cc_start: 0.8178 (t0) cc_final: 0.7903 (t0) REVERT: C 63 ARG cc_start: 0.9336 (ptm160) cc_final: 0.9008 (ptm-80) REVERT: C 66 MET cc_start: 0.9124 (mmm) cc_final: 0.8874 (mmm) REVERT: C 81 ASP cc_start: 0.8336 (t0) cc_final: 0.7596 (t0) REVERT: D 32 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8741 (mmm-85) REVERT: D 78 ARG cc_start: 0.8727 (tpm170) cc_final: 0.8002 (tpp-160) REVERT: D 81 ASP cc_start: 0.8368 (m-30) cc_final: 0.8106 (m-30) REVERT: B 29 MET cc_start: 0.9034 (mpp) cc_final: 0.8769 (mpp) REVERT: B 59 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8588 (mmmt) REVERT: B 63 ARG cc_start: 0.9139 (tmm-80) cc_final: 0.8912 (tmm-80) REVERT: L 482 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7978 (pm20) REVERT: L 502 ASP cc_start: 0.7976 (m-30) cc_final: 0.7733 (m-30) REVERT: L 503 ASP cc_start: 0.8309 (m-30) cc_final: 0.7928 (m-30) REVERT: I 495 ASP cc_start: 0.8367 (t0) cc_final: 0.8137 (t0) REVERT: I 496 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: P 59 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8926 (mptt) REVERT: P 88 ASP cc_start: 0.7909 (t0) cc_final: 0.7645 (t0) REVERT: P 109 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8387 (ptp) REVERT: N 14 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6959 (tm-30) REVERT: N 32 ARG cc_start: 0.8569 (mtp180) cc_final: 0.8202 (mmm-85) REVERT: N 62 HIS cc_start: 0.8634 (t70) cc_final: 0.8257 (t-90) REVERT: N 107 ARG cc_start: 0.7339 (mmt90) cc_final: 0.7015 (mmt90) REVERT: N 117 GLU cc_start: 0.8395 (tm-30) cc_final: 0.8149 (tm-30) REVERT: M 25 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8636 (mm-40) REVERT: M 29 MET cc_start: 0.8699 (mtt) cc_final: 0.8363 (mtp) REVERT: M 32 ARG cc_start: 0.8989 (mmm-85) cc_final: 0.8601 (mmm-85) REVERT: M 59 LYS cc_start: 0.9004 (tptt) cc_final: 0.8779 (tptp) REVERT: M 66 MET cc_start: 0.8996 (mmm) cc_final: 0.8514 (mmm) REVERT: M 103 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7352 (mp10) REVERT: M 123 LYS cc_start: 0.8451 (tppt) cc_final: 0.8109 (tppt) REVERT: O 36 LYS cc_start: 0.9103 (pmmt) cc_final: 0.8897 (pptt) REVERT: O 60 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8355 (mm-30) REVERT: O 63 ARG cc_start: 0.9146 (ttt-90) cc_final: 0.8470 (ttp80) REVERT: O 103 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: O 123 LYS cc_start: 0.8904 (tppp) cc_final: 0.8669 (tptp) REVERT: U 491 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7967 (tm) REVERT: U 493 PHE cc_start: 0.8400 (m-80) cc_final: 0.8191 (m-80) REVERT: T 76 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7745 (tptp) REVERT: R 29 MET cc_start: 0.8593 (mmm) cc_final: 0.8204 (mmm) REVERT: R 62 HIS cc_start: 0.8617 (t-90) cc_final: 0.8334 (t70) REVERT: R 63 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8435 (ttp80) REVERT: R 66 MET cc_start: 0.9044 (mmm) cc_final: 0.8821 (mmm) REVERT: Q 14 GLU cc_start: 0.9234 (tp30) cc_final: 0.8968 (tp30) REVERT: Q 32 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8599 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8531 (pp30) cc_final: 0.7757 (pp30) REVERT: Q 123 LYS cc_start: 0.8563 (tptt) cc_final: 0.8302 (tppt) REVERT: Q 134 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7787 (tm-30) REVERT: S 81 ASP cc_start: 0.8089 (t0) cc_final: 0.7865 (t0) REVERT: W 479 ASN cc_start: 0.8605 (t0) cc_final: 0.8303 (t0) REVERT: W 480 ASP cc_start: 0.8817 (p0) cc_final: 0.8571 (p0) REVERT: W 489 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8452 (mm-30) REVERT: E 59 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8748 (mmtt) REVERT: G 3 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6923 (tpp) REVERT: G 68 GLN cc_start: 0.7814 (mt0) cc_final: 0.7520 (mp10) REVERT: G 81 ASP cc_start: 0.8316 (t0) cc_final: 0.7880 (t0) REVERT: G 134 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: H 32 ARG cc_start: 0.9055 (mmm-85) cc_final: 0.8806 (mmm-85) REVERT: H 60 GLU cc_start: 0.8904 (mp0) cc_final: 0.8635 (mp0) REVERT: H 68 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7130 (tm-30) REVERT: H 81 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: F 29 MET cc_start: 0.9140 (mpp) cc_final: 0.8933 (mpp) REVERT: K 495 ASP cc_start: 0.8874 (t0) cc_final: 0.8670 (t0) REVERT: K 496 PHE cc_start: 0.8447 (m-80) cc_final: 0.7940 (m-80) REVERT: K 500 GLU cc_start: 0.9138 (tt0) cc_final: 0.8896 (tp30) outliers start: 126 outliers final: 52 residues processed: 655 average time/residue: 0.5558 time to fit residues: 414.3396 Evaluate side-chains 597 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 534 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 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 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 T residue 94 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 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 81 ASP 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 36 optimal weight: 6.9990 chunk 137 optimal weight: 0.0070 chunk 209 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 103 GLN A 128 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS 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 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN P 102 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 37 ASN M 69 ASN ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 31 HIS ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 HIS 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 48 ASN ** F 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.109318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.084125 restraints weight = 67356.981| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.31 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 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 = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 20223 Z= 0.281 Angle : 0.716 8.584 27351 Z= 0.369 Chirality : 0.046 0.239 2905 Planarity : 0.004 0.045 3638 Dihedral : 5.733 62.506 2730 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 7.46 % Allowed : 27.17 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2415 helix: 1.89 (0.20), residues: 616 sheet: 0.03 (0.19), residues: 660 loop : 0.51 (0.21), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 63 TYR 0.020 0.002 TYR R 40 PHE 0.023 0.002 PHE S 131 TRP 0.006 0.001 TRP K 509 HIS 0.015 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00647 (20223) covalent geometry : angle 0.71603 (27351) hydrogen bonds : bond 0.04277 ( 892) hydrogen bonds : angle 5.22396 ( 2490) *********************** 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 679 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 518 time to evaluate : 0.809 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 81 ASP cc_start: 0.7399 (t0) cc_final: 0.6996 (t0) REVERT: A 88 ASP cc_start: 0.8379 (t0) cc_final: 0.8087 (t0) REVERT: A 117 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8556 (mm-30) REVERT: A 123 LYS cc_start: 0.9240 (tttm) cc_final: 0.8998 (mmmt) REVERT: C 58 GLN cc_start: 0.8999 (mm110) cc_final: 0.8790 (mm110) REVERT: C 63 ARG cc_start: 0.9390 (ptm160) cc_final: 0.9095 (ptm-80) REVERT: D 28 ASP cc_start: 0.8480 (p0) cc_final: 0.8178 (p0) REVERT: D 29 MET cc_start: 0.9144 (mtm) cc_final: 0.8683 (pmm) REVERT: D 63 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8387 (ttm110) REVERT: D 81 ASP cc_start: 0.8339 (m-30) cc_final: 0.8069 (m-30) REVERT: D 90 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7055 (p) REVERT: B 59 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8626 (mmmt) REVERT: B 63 ARG cc_start: 0.9188 (tmm-80) cc_final: 0.8946 (tmm-80) REVERT: L 502 ASP cc_start: 0.7936 (m-30) cc_final: 0.7557 (t0) REVERT: I 479 ASN cc_start: 0.8781 (t0) cc_final: 0.8501 (t0) REVERT: I 480 ASP cc_start: 0.8879 (t0) cc_final: 0.8657 (t0) REVERT: I 495 ASP cc_start: 0.8565 (t0) cc_final: 0.8280 (t0) REVERT: I 496 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7934 (m-80) REVERT: P 88 ASP cc_start: 0.8384 (t0) cc_final: 0.8114 (t0) REVERT: P 102 ASN cc_start: 0.8871 (t0) cc_final: 0.8544 (t0) REVERT: N 1 MET cc_start: 0.7082 (tpp) cc_final: 0.6742 (tpp) REVERT: N 14 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7340 (tm-30) REVERT: N 29 MET cc_start: 0.8942 (tpt) cc_final: 0.8656 (tpt) REVERT: N 62 HIS cc_start: 0.8713 (t70) cc_final: 0.8312 (t-90) REVERT: N 107 ARG cc_start: 0.7439 (mmt90) cc_final: 0.6965 (mmt90) REVERT: N 117 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8111 (tm-30) REVERT: M 17 ARG cc_start: 0.9062 (ppp80) cc_final: 0.8704 (ptm-80) REVERT: M 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8665 (mmm-85) REVERT: M 59 LYS cc_start: 0.9016 (tptt) cc_final: 0.8755 (tptp) REVERT: M 60 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8324 (mm-30) REVERT: M 88 ASP cc_start: 0.9069 (m-30) cc_final: 0.8716 (t0) REVERT: M 103 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: O 36 LYS cc_start: 0.9203 (pmmt) cc_final: 0.8953 (pptt) REVERT: O 59 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8553 (mmmt) REVERT: O 60 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8396 (mm-30) REVERT: O 103 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7042 (mp10) REVERT: O 123 LYS cc_start: 0.9032 (tppp) cc_final: 0.8797 (tptp) REVERT: U 479 ASN cc_start: 0.8593 (t0) cc_final: 0.8185 (t0) REVERT: U 496 PHE cc_start: 0.8723 (m-80) cc_final: 0.8331 (m-10) REVERT: T 76 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7952 (tptp) REVERT: R 29 MET cc_start: 0.8787 (mmm) cc_final: 0.8402 (mmm) REVERT: R 58 GLN cc_start: 0.8548 (mm110) cc_final: 0.8324 (mm110) REVERT: R 107 ARG cc_start: 0.7120 (mmt90) cc_final: 0.6878 (mmt90) REVERT: Q 93 GLN cc_start: 0.8742 (pp30) cc_final: 0.7893 (pp30) REVERT: Q 123 LYS cc_start: 0.8618 (tptt) cc_final: 0.8392 (ttmt) REVERT: Q 133 TYR cc_start: 0.8882 (m-80) cc_final: 0.8620 (m-80) REVERT: Q 134 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8242 (tm-30) REVERT: S 114 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7734 (mt) REVERT: W 479 ASN cc_start: 0.8635 (t0) cc_final: 0.8375 (t0) REVERT: E 32 ARG cc_start: 0.8775 (mtp180) cc_final: 0.8502 (mtp85) REVERT: E 59 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8727 (mmmt) REVERT: E 76 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7886 (tptp) REVERT: G 25 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8338 (mm-40) REVERT: G 48 ASN cc_start: 0.9211 (t0) cc_final: 0.8901 (p0) REVERT: G 66 MET cc_start: 0.9243 (mmm) cc_final: 0.9026 (mmm) REVERT: G 68 GLN cc_start: 0.7841 (mt0) cc_final: 0.7439 (mp10) REVERT: G 128 ASN cc_start: 0.8868 (OUTLIER) cc_final: 0.8635 (m110) REVERT: H 17 ARG cc_start: 0.9001 (ppp80) cc_final: 0.8634 (ptm-80) REVERT: H 60 GLU cc_start: 0.8958 (mp0) cc_final: 0.8617 (mp0) REVERT: H 68 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7575 (tm-30) REVERT: H 81 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: H 106 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (mtp180) REVERT: K 495 ASP cc_start: 0.8957 (t0) cc_final: 0.8682 (t0) REVERT: K 496 PHE cc_start: 0.8779 (m-80) cc_final: 0.8163 (m-80) REVERT: K 500 GLU cc_start: 0.9126 (tt0) cc_final: 0.8735 (tp30) REVERT: K 503 ASP cc_start: 0.9412 (p0) cc_final: 0.8898 (p0) outliers start: 161 outliers final: 71 residues processed: 619 average time/residue: 0.6017 time to fit residues: 421.5304 Evaluate side-chains 570 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 489 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 53 ASP 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 30 LEU 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 L residue 479 ASN 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 94 VAL Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain N residue 92 VAL 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 103 GLN 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 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 76 LYS 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 75 THR Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 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 E residue 33 PHE 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 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 G residue 128 ASN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 81 ASP 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 137 VAL Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain K residue 474 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 196 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 128 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 72 ASN ** 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 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 ASN T 42 HIS T 68 GLN ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 ASN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN Q 128 ASN S 48 ASN ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089286 restraints weight = 68411.648| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 5.39 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 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 = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20223 Z= 0.135 Angle : 0.669 11.594 27351 Z= 0.335 Chirality : 0.045 0.196 2905 Planarity : 0.004 0.049 3638 Dihedral : 5.344 56.347 2725 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.38 % Allowed : 30.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.18), residues: 2415 helix: 1.92 (0.20), residues: 616 sheet: -0.10 (0.18), residues: 724 loop : 0.65 (0.22), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 63 TYR 0.017 0.002 TYR N 20 PHE 0.031 0.002 PHE E 33 TRP 0.002 0.000 TRP U 509 HIS 0.010 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00310 (20223) covalent geometry : angle 0.66897 (27351) hydrogen bonds : bond 0.03505 ( 892) hydrogen bonds : angle 4.98426 ( 2490) *********************** 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 680 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 564 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7490 (t0) cc_final: 0.7110 (t0) REVERT: A 88 ASP cc_start: 0.8411 (t0) cc_final: 0.8069 (t0) REVERT: A 93 GLN cc_start: 0.8436 (tt0) cc_final: 0.8172 (tt0) REVERT: A 117 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8602 (mm-30) REVERT: A 123 LYS cc_start: 0.9244 (tttm) cc_final: 0.8874 (mmmt) REVERT: C 63 ARG cc_start: 0.9371 (ptm160) cc_final: 0.9058 (ptm-80) REVERT: D 17 ARG cc_start: 0.9022 (ppp80) cc_final: 0.8724 (ptm-80) REVERT: D 28 ASP cc_start: 0.8475 (p0) cc_final: 0.8203 (p0) REVERT: D 29 MET cc_start: 0.9063 (mtm) cc_final: 0.8785 (pmm) REVERT: D 32 ARG cc_start: 0.8834 (mtm180) cc_final: 0.8166 (mtp180) REVERT: D 78 ARG cc_start: 0.8639 (tpm170) cc_final: 0.8001 (tpp-160) REVERT: D 81 ASP cc_start: 0.8424 (m-30) cc_final: 0.8074 (m-30) REVERT: D 90 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7159 (p) REVERT: D 93 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8250 (tm-30) REVERT: B 29 MET cc_start: 0.9069 (mpp) cc_final: 0.8839 (mpp) REVERT: B 59 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8598 (mmmt) REVERT: B 63 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8910 (tmm-80) REVERT: L 477 ASP cc_start: 0.8693 (p0) cc_final: 0.8475 (p0) REVERT: L 502 ASP cc_start: 0.7873 (m-30) cc_final: 0.7543 (p0) REVERT: I 479 ASN cc_start: 0.8791 (t0) cc_final: 0.8504 (t0) REVERT: I 480 ASP cc_start: 0.8764 (t0) cc_final: 0.8536 (t0) REVERT: I 484 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8311 (mm-30) REVERT: I 495 ASP cc_start: 0.8552 (t70) cc_final: 0.8262 (t0) REVERT: P 13 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7265 (ttp80) REVERT: P 88 ASP cc_start: 0.8244 (t0) cc_final: 0.7895 (t0) REVERT: P 123 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8263 (tptp) REVERT: N 1 MET cc_start: 0.7240 (tpp) cc_final: 0.6974 (tmm) REVERT: N 3 MET cc_start: 0.6965 (tpp) cc_final: 0.6686 (tpp) REVERT: N 14 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7219 (tm-30) REVERT: N 62 HIS cc_start: 0.8704 (t70) cc_final: 0.8345 (t-90) REVERT: N 117 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8162 (tm-30) REVERT: M 17 ARG cc_start: 0.9025 (ppp80) cc_final: 0.8674 (ptm-80) REVERT: M 25 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8620 (mm-40) REVERT: M 32 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8544 (mmm-85) REVERT: M 103 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7317 (mp10) REVERT: M 117 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: O 36 LYS cc_start: 0.9111 (pmmt) cc_final: 0.8851 (pptt) REVERT: O 59 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8565 (mmmt) REVERT: O 60 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8338 (mm-30) REVERT: O 63 ARG cc_start: 0.9215 (ttt-90) cc_final: 0.8510 (ttp80) REVERT: O 103 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.6984 (mp10) REVERT: U 479 ASN cc_start: 0.8561 (t0) cc_final: 0.8154 (t0) REVERT: T 76 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8005 (tptt) REVERT: R 29 MET cc_start: 0.8861 (mmm) cc_final: 0.8474 (mmm) REVERT: R 63 ARG cc_start: 0.9275 (mtp-110) cc_final: 0.8802 (tpm170) REVERT: R 68 GLN cc_start: 0.7791 (mp10) cc_final: 0.7343 (mp10) REVERT: Q 93 GLN cc_start: 0.8678 (pp30) cc_final: 0.8017 (pp30) REVERT: Q 123 LYS cc_start: 0.8651 (tptt) cc_final: 0.8443 (ttmt) REVERT: Q 134 GLN cc_start: 0.8441 (tm-30) cc_final: 0.8015 (tm-30) REVERT: Q 136 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: W 479 ASN cc_start: 0.8624 (t0) cc_final: 0.8341 (t0) REVERT: W 496 PHE cc_start: 0.8525 (m-80) cc_final: 0.8231 (m-10) REVERT: W 500 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8792 (pp20) REVERT: E 32 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8033 (mtp180) REVERT: E 59 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8749 (mmtt) REVERT: E 76 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7882 (tptt) REVERT: G 3 MET cc_start: 0.7381 (mmm) cc_final: 0.7082 (tpp) REVERT: G 48 ASN cc_start: 0.9256 (t0) cc_final: 0.8950 (p0) REVERT: G 68 GLN cc_start: 0.7732 (mt0) cc_final: 0.7368 (mp10) REVERT: G 103 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8742 (mp10) REVERT: G 134 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8221 (pt0) REVERT: H 17 ARG cc_start: 0.8983 (ppp80) cc_final: 0.8578 (ptm-80) REVERT: H 56 TYR cc_start: 0.9029 (m-80) cc_final: 0.8674 (m-80) REVERT: H 60 GLU cc_start: 0.8952 (mp0) cc_final: 0.8615 (mp0) REVERT: H 68 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7450 (tm-30) REVERT: H 81 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: H 106 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7857 (mtp180) REVERT: F 29 MET cc_start: 0.9070 (mpp) cc_final: 0.8829 (mpp) REVERT: F 53 ASP cc_start: 0.8899 (p0) cc_final: 0.8463 (p0) REVERT: F 103 GLN cc_start: 0.8065 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: K 495 ASP cc_start: 0.8918 (t0) cc_final: 0.8603 (t0) REVERT: K 496 PHE cc_start: 0.8864 (m-80) cc_final: 0.8347 (m-80) REVERT: K 500 GLU cc_start: 0.9231 (tt0) cc_final: 0.8650 (tp30) REVERT: K 503 ASP cc_start: 0.9354 (p0) cc_final: 0.8723 (p0) outliers start: 116 outliers final: 52 residues processed: 644 average time/residue: 0.5921 time to fit residues: 431.3977 Evaluate side-chains 607 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 538 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 P residue 13 ARG 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 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 M residue 117 GLU Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 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 76 LYS Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 114 LEU Chi-restraints excluded: chain W residue 473 ILE Chi-restraints excluded: chain W residue 500 GLU 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 70 PHE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain G residue 134 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 81 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain J residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 107 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 171 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 93 GLN ** 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** B 128 ASN P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 103 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 102 ASN S 128 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.110649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087154 restraints weight = 49024.394| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.53 r_work: 0.3255 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3022 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= 0.212 Angle : 0.705 10.451 27351 Z= 0.357 Chirality : 0.046 0.219 2905 Planarity : 0.004 0.048 3638 Dihedral : 5.334 55.402 2721 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 6.35 % Allowed : 29.58 % Favored : 64.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.18), residues: 2415 helix: 1.92 (0.20), residues: 620 sheet: -0.32 (0.18), residues: 786 loop : 0.85 (0.23), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 63 TYR 0.024 0.002 TYR G 40 PHE 0.026 0.002 PHE D 15 TRP 0.002 0.001 TRP K 509 HIS 0.011 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00494 (20223) covalent geometry : angle 0.70473 (27351) hydrogen bonds : bond 0.03832 ( 892) hydrogen bonds : angle 5.03509 ( 2490) *********************** 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 675 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 538 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7607 (t0) cc_final: 0.7111 (OUTLIER) REVERT: A 88 ASP cc_start: 0.8483 (t0) cc_final: 0.8161 (t0) REVERT: A 132 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7623 (mtp85) REVERT: C 63 ARG cc_start: 0.9425 (ptm160) cc_final: 0.9106 (ptm-80) REVERT: D 17 ARG cc_start: 0.9136 (ppp80) cc_final: 0.8798 (ptm-80) REVERT: D 32 ARG cc_start: 0.8954 (mtm180) cc_final: 0.8365 (mtp180) REVERT: D 81 ASP cc_start: 0.8621 (m-30) cc_final: 0.8183 (m-30) REVERT: D 90 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7044 (p) REVERT: D 93 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8253 (tm-30) REVERT: B 59 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8611 (mmmt) REVERT: B 63 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8976 (tmm-80) REVERT: B 113 VAL cc_start: 0.9186 (t) cc_final: 0.8971 (p) REVERT: L 502 ASP cc_start: 0.7990 (m-30) cc_final: 0.7700 (p0) REVERT: I 479 ASN cc_start: 0.8963 (t0) cc_final: 0.8693 (t0) REVERT: I 495 ASP cc_start: 0.8736 (t70) cc_final: 0.8500 (t0) REVERT: I 497 LEU cc_start: 0.9081 (mm) cc_final: 0.8706 (pp) REVERT: P 88 ASP cc_start: 0.8551 (t0) cc_final: 0.8085 (t0) REVERT: P 102 ASN cc_start: 0.9118 (t0) cc_final: 0.8834 (t0) REVERT: P 123 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8265 (tptp) REVERT: N 1 MET cc_start: 0.7182 (tpp) cc_final: 0.6848 (mmm) REVERT: N 3 MET cc_start: 0.7350 (tpp) cc_final: 0.7056 (tpp) REVERT: N 29 MET cc_start: 0.8950 (tpt) cc_final: 0.8453 (tpt) REVERT: N 62 HIS cc_start: 0.8671 (t70) cc_final: 0.8410 (t-90) REVERT: N 117 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8267 (tm-30) REVERT: M 32 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8694 (mmm-85) REVERT: M 63 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8253 (ttm110) REVERT: M 103 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: O 36 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8916 (pptt) REVERT: O 59 LYS cc_start: 0.8813 (mmmt) cc_final: 0.8598 (mmmt) REVERT: O 60 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8512 (mm-30) REVERT: O 63 ARG cc_start: 0.9269 (ttt-90) cc_final: 0.8610 (ttp80) REVERT: O 103 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: U 479 ASN cc_start: 0.8672 (t0) cc_final: 0.8299 (t0) REVERT: U 496 PHE cc_start: 0.8836 (m-10) cc_final: 0.8372 (m-10) REVERT: T 76 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8211 (tptt) REVERT: Q 32 ARG cc_start: 0.9130 (mmm-85) cc_final: 0.8819 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8833 (pp30) cc_final: 0.8136 (pp30) REVERT: Q 101 ASN cc_start: 0.8791 (m-40) cc_final: 0.8506 (m110) REVERT: Q 103 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: Q 123 LYS cc_start: 0.8620 (tptt) cc_final: 0.8410 (ttmt) REVERT: Q 134 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8126 (tm130) REVERT: Q 136 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8689 (pp20) REVERT: S 114 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8034 (mt) REVERT: W 479 ASN cc_start: 0.8697 (t0) cc_final: 0.8410 (t0) REVERT: E 14 GLU cc_start: 0.8981 (tp30) cc_final: 0.8747 (tp30) REVERT: E 59 LYS cc_start: 0.9260 (mmmm) cc_final: 0.8884 (mmmt) REVERT: E 76 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8069 (tptp) REVERT: E 102 ASN cc_start: 0.9245 (t0) cc_final: 0.8906 (t0) REVERT: G 48 ASN cc_start: 0.9253 (t0) cc_final: 0.8932 (p0) REVERT: G 81 ASP cc_start: 0.8393 (t0) cc_final: 0.7836 (t0) REVERT: G 103 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8752 (mp10) REVERT: H 17 ARG cc_start: 0.9086 (ppp80) cc_final: 0.8880 (ppp80) REVERT: H 36 LYS cc_start: 0.8882 (tppt) cc_final: 0.8669 (ttmm) REVERT: H 60 GLU cc_start: 0.9205 (mp0) cc_final: 0.8866 (mp0) REVERT: H 68 GLN cc_start: 0.8310 (tm-30) cc_final: 0.8037 (tm-30) REVERT: H 81 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: H 106 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8003 (mtp180) REVERT: F 53 ASP cc_start: 0.9170 (p0) cc_final: 0.8754 (p0) REVERT: F 101 ASN cc_start: 0.9211 (t0) cc_final: 0.8637 (t0) REVERT: F 103 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: K 479 ASN cc_start: 0.9099 (t0) cc_final: 0.8802 (t0) REVERT: K 480 ASP cc_start: 0.9152 (t0) cc_final: 0.8889 (t0) REVERT: K 495 ASP cc_start: 0.8915 (t0) cc_final: 0.8564 (t0) REVERT: K 496 PHE cc_start: 0.8981 (m-80) cc_final: 0.8646 (m-80) REVERT: K 500 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: K 503 ASP cc_start: 0.9367 (p0) cc_final: 0.8760 (p0) outliers start: 137 outliers final: 74 residues processed: 625 average time/residue: 0.5776 time to fit residues: 407.9896 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 : 0.822 ------------------------------------------------------------------------------- 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 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 63 ARG Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 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 P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 73 CYS Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 103 GLN Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 39 SER 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 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 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 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 90 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 109 MET Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 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 41 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 95 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 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 81 ASP 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 488 SER Chi-restraints excluded: chain J residue 506 ASP Chi-restraints excluded: chain K residue 485 SER 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 3 optimal weight: 8.9990 chunk 169 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 204 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 178 optimal weight: 30.0000 chunk 107 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 69 ASN ** 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 N 24 ASN 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 ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 HIS ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 62 HIS ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN H 31 HIS H 42 HIS H 128 ASN ** F 24 ASN ** 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 = 0.3874 r_free = 0.3874 target = 0.114168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.088767 restraints weight = 85468.879| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 5.92 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3458 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3458 r_free = 0.3458 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3458 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20223 Z= 0.142 Angle : 0.705 11.774 27351 Z= 0.352 Chirality : 0.045 0.198 2905 Planarity : 0.004 0.052 3638 Dihedral : 5.094 56.672 2719 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.24 % Allowed : 31.62 % Favored : 63.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.18), residues: 2415 helix: 1.88 (0.20), residues: 618 sheet: -0.14 (0.18), residues: 724 loop : 0.79 (0.22), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 63 TYR 0.018 0.001 TYR G 20 PHE 0.020 0.002 PHE D 15 TRP 0.003 0.000 TRP W 509 HIS 0.009 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00327 (20223) covalent geometry : angle 0.70465 (27351) hydrogen bonds : bond 0.03517 ( 892) hydrogen bonds : angle 4.97076 ( 2490) *********************** 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 675 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 562 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7578 (t0) cc_final: 0.7127 (t0) REVERT: A 88 ASP cc_start: 0.8478 (t0) cc_final: 0.8146 (t0) REVERT: A 123 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8985 (tptm) REVERT: A 132 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7565 (mtp85) REVERT: C 32 ARG cc_start: 0.8796 (ttp80) cc_final: 0.8060 (ttp80) REVERT: C 63 ARG cc_start: 0.9389 (ptm160) cc_final: 0.9066 (ptm-80) REVERT: D 32 ARG cc_start: 0.8853 (mtm180) cc_final: 0.8224 (mtp180) REVERT: D 81 ASP cc_start: 0.8433 (m-30) cc_final: 0.7704 (m-30) REVERT: D 93 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7804 (tm-30) REVERT: D 135 ASP cc_start: 0.8411 (m-30) cc_final: 0.7943 (m-30) REVERT: B 29 MET cc_start: 0.9073 (mpp) cc_final: 0.8817 (mpp) REVERT: B 59 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8622 (mmmt) REVERT: B 63 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8877 (tmm-80) REVERT: B 101 ASN cc_start: 0.9314 (t0) cc_final: 0.8675 (t0) REVERT: L 502 ASP cc_start: 0.7897 (m-30) cc_final: 0.7543 (t0) REVERT: I 479 ASN cc_start: 0.8886 (t0) cc_final: 0.8594 (t0) REVERT: I 495 ASP cc_start: 0.8681 (t70) cc_final: 0.8476 (t0) REVERT: I 497 LEU cc_start: 0.9038 (mm) cc_final: 0.8652 (pp) REVERT: I 500 GLU cc_start: 0.9227 (tt0) cc_final: 0.8986 (tt0) REVERT: P 29 MET cc_start: 0.8771 (mmp) cc_final: 0.8470 (mmp) REVERT: P 88 ASP cc_start: 0.8489 (t0) cc_final: 0.7974 (t0) REVERT: P 123 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8451 (tptm) REVERT: N 1 MET cc_start: 0.7347 (tpp) cc_final: 0.7064 (mmm) REVERT: N 3 MET cc_start: 0.7031 (tpp) cc_final: 0.6676 (tpp) REVERT: N 14 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7137 (tm-30) REVERT: N 29 MET cc_start: 0.8938 (tpt) cc_final: 0.8718 (tpt) REVERT: N 62 HIS cc_start: 0.8651 (t70) cc_final: 0.8419 (t-90) REVERT: N 117 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8209 (tm-30) REVERT: M 17 ARG cc_start: 0.9017 (ppp80) cc_final: 0.8776 (ptm-80) REVERT: M 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8543 (mmm-85) REVERT: M 93 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8684 (tm-30) REVERT: O 36 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8856 (pptt) REVERT: O 59 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8569 (mmmt) REVERT: O 60 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8377 (mm-30) REVERT: O 63 ARG cc_start: 0.9173 (ttt-90) cc_final: 0.8484 (ttp80) REVERT: O 103 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: U 479 ASN cc_start: 0.8602 (t0) cc_final: 0.8268 (t0) REVERT: T 76 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8144 (tptt) REVERT: R 29 MET cc_start: 0.8988 (mmm) cc_final: 0.8432 (tpt) REVERT: Q 14 GLU cc_start: 0.9328 (tp30) cc_final: 0.8879 (tp30) REVERT: Q 29 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: Q 32 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8713 (mmm-85) REVERT: Q 63 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8115 (ttm110) REVERT: Q 66 MET cc_start: 0.8829 (mmp) cc_final: 0.8627 (mmm) REVERT: Q 93 GLN cc_start: 0.8673 (pp30) cc_final: 0.7937 (pp30) REVERT: Q 123 LYS cc_start: 0.8711 (tptt) cc_final: 0.8506 (ttmt) REVERT: Q 134 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7909 (tm130) REVERT: Q 136 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: W 479 ASN cc_start: 0.8632 (t0) cc_final: 0.8353 (t0) REVERT: E 59 LYS cc_start: 0.9133 (mmmm) cc_final: 0.8711 (mmmt) REVERT: E 76 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7826 (tptp) REVERT: G 3 MET cc_start: 0.7222 (mmm) cc_final: 0.6940 (tpp) REVERT: G 48 ASN cc_start: 0.9265 (t0) cc_final: 0.8942 (p0) REVERT: G 68 GLN cc_start: 0.7679 (mt0) cc_final: 0.7241 (mp10) REVERT: G 103 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: H 17 ARG cc_start: 0.8989 (ppp80) cc_final: 0.8764 (ppp80) REVERT: H 36 LYS cc_start: 0.8814 (tppt) cc_final: 0.8612 (ttmm) REVERT: H 60 GLU cc_start: 0.9004 (mp0) cc_final: 0.8622 (mp0) REVERT: H 68 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7573 (tm-30) REVERT: H 81 ASP cc_start: 0.8591 (t0) cc_final: 0.8291 (m-30) REVERT: H 100 ASN cc_start: 0.8887 (p0) cc_final: 0.8674 (p0) REVERT: F 29 MET cc_start: 0.9068 (mpp) cc_final: 0.8837 (mpp) REVERT: F 53 ASP cc_start: 0.8920 (p0) cc_final: 0.8491 (p0) REVERT: F 103 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: J 495 ASP cc_start: 0.8183 (m-30) cc_final: 0.7876 (p0) REVERT: K 479 ASN cc_start: 0.8982 (t0) cc_final: 0.8689 (t0) REVERT: K 480 ASP cc_start: 0.9071 (t0) cc_final: 0.8776 (t0) REVERT: K 495 ASP cc_start: 0.8891 (t0) cc_final: 0.8490 (t0) REVERT: K 500 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8417 (tm-30) outliers start: 113 outliers final: 61 residues processed: 639 average time/residue: 0.6118 time to fit residues: 442.5626 Evaluate side-chains 590 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 516 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 95 MET 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 L residue 473 ILE Chi-restraints excluded: chain L residue 479 ASN 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 55 VAL 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 O residue 10 LEU Chi-restraints excluded: chain O residue 36 LYS 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 479 ASN Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain T residue 53 ASP Chi-restraints excluded: chain T residue 76 LYS Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain Q residue 10 LEU Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 71 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain 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 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 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 7.9990 chunk 143 optimal weight: 0.2980 chunk 196 optimal weight: 7.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 GLN ** 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** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS H 101 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.113672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089900 restraints weight = 53229.603| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.74 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 = 0.44 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: 0.8001 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20223 Z= 0.157 Angle : 0.711 10.312 27351 Z= 0.357 Chirality : 0.045 0.195 2905 Planarity : 0.004 0.055 3638 Dihedral : 5.067 57.819 2719 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.47 % Allowed : 32.27 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.18), residues: 2415 helix: 1.89 (0.20), residues: 618 sheet: -0.17 (0.18), residues: 728 loop : 0.82 (0.22), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 63 TYR 0.027 0.002 TYR R 40 PHE 0.027 0.002 PHE D 15 TRP 0.002 0.000 TRP W 509 HIS 0.018 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00370 (20223) covalent geometry : angle 0.71065 (27351) hydrogen bonds : bond 0.03549 ( 892) hydrogen bonds : angle 4.92844 ( 2490) *********************** 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 645 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 527 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7582 (t0) cc_final: 0.7102 (OUTLIER) REVERT: A 88 ASP cc_start: 0.8503 (t0) cc_final: 0.8121 (t0) REVERT: A 132 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7519 (mtp85) REVERT: C 32 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8101 (ttp80) REVERT: C 63 ARG cc_start: 0.9386 (ptm160) cc_final: 0.9073 (ptm-80) REVERT: D 17 ARG cc_start: 0.8986 (ppp80) cc_final: 0.8695 (ptm-80) REVERT: D 32 ARG cc_start: 0.8842 (mtm180) cc_final: 0.8225 (mtp180) REVERT: D 81 ASP cc_start: 0.8361 (m-30) cc_final: 0.7961 (m-30) REVERT: D 90 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7032 (p) REVERT: D 93 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8191 (tm130) REVERT: D 135 ASP cc_start: 0.8389 (m-30) cc_final: 0.7969 (m-30) REVERT: B 29 MET cc_start: 0.9084 (mpp) cc_final: 0.8852 (mpp) REVERT: B 59 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8594 (mmmt) REVERT: B 63 ARG cc_start: 0.9171 (OUTLIER) cc_final: 0.8865 (tmm-80) REVERT: B 101 ASN cc_start: 0.9291 (t0) cc_final: 0.8620 (t0) REVERT: L 502 ASP cc_start: 0.7867 (m-30) cc_final: 0.7532 (t0) REVERT: I 479 ASN cc_start: 0.8920 (t0) cc_final: 0.8161 (t0) REVERT: I 480 ASP cc_start: 0.8870 (t0) cc_final: 0.8008 (p0) REVERT: I 495 ASP cc_start: 0.8696 (t70) cc_final: 0.8486 (t0) REVERT: I 497 LEU cc_start: 0.9033 (mm) cc_final: 0.8624 (pp) REVERT: I 500 GLU cc_start: 0.9243 (tt0) cc_final: 0.8966 (tt0) REVERT: P 29 MET cc_start: 0.8782 (mmp) cc_final: 0.8488 (mmp) REVERT: P 88 ASP cc_start: 0.8497 (t0) cc_final: 0.7933 (t0) REVERT: P 123 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8432 (tptm) REVERT: P 132 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7706 (mtp85) REVERT: N 1 MET cc_start: 0.7364 (tpp) cc_final: 0.7039 (mmm) REVERT: N 3 MET cc_start: 0.7076 (tpp) cc_final: 0.6695 (tpp) REVERT: N 29 MET cc_start: 0.8962 (tpt) cc_final: 0.8414 (tpt) REVERT: N 62 HIS cc_start: 0.8663 (t70) cc_final: 0.8416 (t-90) REVERT: N 107 ARG cc_start: 0.7513 (mmt90) cc_final: 0.7109 (mmt90) REVERT: N 109 MET cc_start: 0.8099 (mtp) cc_final: 0.7858 (mtp) REVERT: N 117 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8170 (tm-30) REVERT: M 17 ARG cc_start: 0.8990 (ppp80) cc_final: 0.8726 (ppp80) REVERT: M 32 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8547 (mmm-85) REVERT: M 93 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8408 (tm-30) REVERT: O 59 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8521 (mmmt) REVERT: O 60 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8414 (mm-30) REVERT: O 63 ARG cc_start: 0.9159 (ttt-90) cc_final: 0.8471 (ttp80) REVERT: O 103 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7224 (mp10) REVERT: V 502 ASP cc_start: 0.8244 (m-30) cc_final: 0.7416 (p0) REVERT: U 479 ASN cc_start: 0.8621 (t0) cc_final: 0.8315 (t0) REVERT: U 496 PHE cc_start: 0.8733 (m-10) cc_final: 0.8522 (m-10) REVERT: T 76 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8140 (tptt) REVERT: T 88 ASP cc_start: 0.8100 (t0) cc_final: 0.7878 (t0) REVERT: R 29 MET cc_start: 0.8975 (mmm) cc_final: 0.8414 (tpt) REVERT: Q 14 GLU cc_start: 0.9318 (tp30) cc_final: 0.8866 (tp30) REVERT: Q 29 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8115 (mtt) REVERT: Q 32 ARG cc_start: 0.9001 (mmm-85) cc_final: 0.8694 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8699 (pp30) cc_final: 0.8023 (pp30) REVERT: Q 123 LYS cc_start: 0.8721 (tptt) cc_final: 0.8518 (ttmt) REVERT: Q 134 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7963 (tm130) REVERT: Q 136 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8616 (pp20) REVERT: S 63 ARG cc_start: 0.9191 (tmm-80) cc_final: 0.8970 (ttp80) REVERT: W 479 ASN cc_start: 0.8599 (t0) cc_final: 0.8312 (t0) REVERT: W 496 PHE cc_start: 0.8680 (m-80) cc_final: 0.8200 (m-10) REVERT: E 59 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8708 (mmmt) REVERT: E 76 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7673 (tptp) REVERT: E 102 ASN cc_start: 0.8861 (t0) cc_final: 0.8430 (t0) REVERT: G 48 ASN cc_start: 0.9234 (t0) cc_final: 0.8937 (p0) REVERT: G 68 GLN cc_start: 0.7678 (mt0) cc_final: 0.7207 (mp10) REVERT: G 103 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8788 (mp10) REVERT: H 17 ARG cc_start: 0.8987 (ppp80) cc_final: 0.8574 (ppp80) REVERT: H 60 GLU cc_start: 0.8974 (mp0) cc_final: 0.8649 (mp0) REVERT: H 68 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7689 (tm-30) REVERT: H 81 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: H 106 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7963 (mtp180) REVERT: F 29 MET cc_start: 0.9066 (mpp) cc_final: 0.8776 (mpp) REVERT: F 53 ASP cc_start: 0.8868 (p0) cc_final: 0.8435 (p0) REVERT: F 103 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: J 495 ASP cc_start: 0.8201 (m-30) cc_final: 0.7889 (p0) REVERT: K 479 ASN cc_start: 0.8985 (t0) cc_final: 0.8682 (t0) REVERT: K 480 ASP cc_start: 0.9029 (t0) cc_final: 0.8736 (t0) REVERT: K 495 ASP cc_start: 0.8862 (t0) cc_final: 0.8495 (t0) REVERT: K 496 PHE cc_start: 0.8930 (m-80) cc_final: 0.8686 (m-80) REVERT: K 500 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8547 (tp30) REVERT: K 503 ASP cc_start: 0.9379 (p0) cc_final: 0.8753 (p0) outliers start: 118 outliers final: 64 residues processed: 600 average time/residue: 0.6056 time to fit residues: 410.7923 Evaluate side-chains 596 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 518 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 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 L residue 473 ILE Chi-restraints excluded: chain L residue 479 ASN Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain I residue 504 LEU Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 132 ARG 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 41 VAL Chi-restraints excluded: chain O residue 10 LEU Chi-restraints excluded: chain O residue 39 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 103 GLN Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain V residue 473 ILE Chi-restraints excluded: chain V residue 479 ASN Chi-restraints excluded: chain V residue 492 THR Chi-restraints excluded: chain U residue 487 SER Chi-restraints excluded: chain T residue 76 LYS 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 99 SER Chi-restraints excluded: chain Q residue 29 MET Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 77 ILE Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 103 GLN Chi-restraints excluded: chain Q residue 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 76 LYS 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 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 81 ASP 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 J residue 473 ILE Chi-restraints excluded: chain J residue 488 SER Chi-restraints excluded: chain K residue 485 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 54 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 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 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN R 68 GLN Q 69 ASN Q 101 ASN ** 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** G 72 ASN H 42 HIS ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.115104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.090439 restraints weight = 69868.601| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 5.42 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20223 Z= 0.146 Angle : 0.736 12.626 27351 Z= 0.364 Chirality : 0.045 0.240 2905 Planarity : 0.004 0.053 3638 Dihedral : 4.934 59.019 2719 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.78 % Allowed : 33.57 % Favored : 61.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.18), residues: 2415 helix: 1.87 (0.21), residues: 618 sheet: -0.14 (0.18), residues: 728 loop : 0.87 (0.23), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 63 TYR 0.016 0.001 TYR G 20 PHE 0.024 0.002 PHE D 15 TRP 0.003 0.000 TRP W 509 HIS 0.016 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00342 (20223) covalent geometry : angle 0.73627 (27351) hydrogen bonds : bond 0.03464 ( 892) hydrogen bonds : angle 4.88995 ( 2490) *********************** 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: 103 poor density : 550 time to evaluate : 0.841 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 81 ASP cc_start: 0.7572 (t0) cc_final: 0.7081 (OUTLIER) REVERT: A 88 ASP cc_start: 0.8496 (t0) cc_final: 0.8147 (t0) REVERT: A 132 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7445 (mtp85) REVERT: C 36 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8582 (mmpt) REVERT: C 63 ARG cc_start: 0.9390 (ptm160) cc_final: 0.9071 (ptm-80) REVERT: D 32 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8235 (mtp180) REVERT: D 81 ASP cc_start: 0.8371 (m-30) cc_final: 0.7740 (m-30) REVERT: D 93 GLN cc_start: 0.8424 (tm-30) cc_final: 0.7729 (tm-30) REVERT: D 135 ASP cc_start: 0.8341 (m-30) cc_final: 0.7894 (m-30) REVERT: B 29 MET cc_start: 0.9094 (mpp) cc_final: 0.8876 (mpp) REVERT: B 59 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8628 (mmmt) REVERT: B 101 ASN cc_start: 0.9254 (t0) cc_final: 0.8576 (t0) REVERT: L 502 ASP cc_start: 0.7866 (m-30) cc_final: 0.7537 (t0) REVERT: I 479 ASN cc_start: 0.8866 (t0) cc_final: 0.8098 (t0) REVERT: I 480 ASP cc_start: 0.8806 (t0) cc_final: 0.7892 (p0) REVERT: I 484 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8509 (mm-30) REVERT: I 495 ASP cc_start: 0.8686 (t70) cc_final: 0.8378 (t0) REVERT: P 88 ASP cc_start: 0.8362 (t0) cc_final: 0.7877 (t0) REVERT: P 102 ASN cc_start: 0.8770 (t0) cc_final: 0.8482 (t0) REVERT: P 123 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8389 (tptm) REVERT: N 1 MET cc_start: 0.7453 (tpp) cc_final: 0.7038 (tmm) REVERT: N 3 MET cc_start: 0.6974 (tpp) cc_final: 0.6591 (tpp) REVERT: N 29 MET cc_start: 0.8954 (tpt) cc_final: 0.8466 (tpt) REVERT: N 62 HIS cc_start: 0.8655 (t70) cc_final: 0.8399 (t-90) REVERT: N 68 GLN cc_start: 0.8130 (mp10) cc_final: 0.7719 (mp10) REVERT: N 109 MET cc_start: 0.8272 (mtp) cc_final: 0.7755 (mtp) REVERT: N 117 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8205 (tm-30) REVERT: N 123 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8095 (tppp) REVERT: M 17 ARG cc_start: 0.8992 (ppp80) cc_final: 0.8693 (ppp80) REVERT: M 32 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8634 (mmm-85) REVERT: M 93 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8327 (tm-30) REVERT: M 103 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: O 59 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8511 (mmmt) REVERT: O 60 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8397 (mm-30) REVERT: O 63 ARG cc_start: 0.9139 (ttt-90) cc_final: 0.8471 (ttp80) REVERT: O 103 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: V 477 ASP cc_start: 0.8634 (p0) cc_final: 0.7873 (p0) REVERT: V 502 ASP cc_start: 0.8243 (m-30) cc_final: 0.7396 (p0) REVERT: U 479 ASN cc_start: 0.8632 (t0) cc_final: 0.8312 (t0) REVERT: U 496 PHE cc_start: 0.8719 (m-10) cc_final: 0.8405 (m-10) REVERT: U 500 GLU cc_start: 0.8994 (tt0) cc_final: 0.8684 (tp30) REVERT: T 88 ASP cc_start: 0.8123 (t0) cc_final: 0.7856 (t0) REVERT: R 29 MET cc_start: 0.8937 (mmm) cc_final: 0.8298 (tpt) REVERT: R 36 LYS cc_start: 0.8985 (pptt) cc_final: 0.8637 (mmpt) REVERT: Q 14 GLU cc_start: 0.9339 (tp30) cc_final: 0.8814 (tp30) REVERT: Q 28 ASP cc_start: 0.8941 (p0) cc_final: 0.8682 (p0) REVERT: Q 32 ARG cc_start: 0.9005 (mmm-85) cc_final: 0.8307 (mmm-85) REVERT: Q 93 GLN cc_start: 0.8662 (pp30) cc_final: 0.7989 (pp30) REVERT: Q 123 LYS cc_start: 0.8723 (tptt) cc_final: 0.8512 (ttmt) REVERT: Q 134 GLN cc_start: 0.8337 (tm-30) cc_final: 0.8090 (tm-30) REVERT: Q 136 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8640 (pp20) REVERT: S 63 ARG cc_start: 0.9206 (tmm-80) cc_final: 0.8965 (ttp80) REVERT: S 81 ASP cc_start: 0.8076 (t0) cc_final: 0.7723 (t0) REVERT: W 479 ASN cc_start: 0.8614 (t0) cc_final: 0.8330 (t0) REVERT: W 496 PHE cc_start: 0.8731 (m-80) cc_final: 0.8291 (m-10) REVERT: E 59 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8718 (mmmt) REVERT: E 76 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7614 (tptp) REVERT: E 109 MET cc_start: 0.9018 (ptm) cc_final: 0.8795 (ptp) REVERT: G 29 MET cc_start: 0.8779 (mmm) cc_final: 0.8519 (mtp) REVERT: G 48 ASN cc_start: 0.9251 (t0) cc_final: 0.8955 (p0) REVERT: G 68 GLN cc_start: 0.7639 (mt0) cc_final: 0.7194 (mp10) REVERT: H 17 ARG cc_start: 0.8983 (ppp80) cc_final: 0.8598 (ppp80) REVERT: H 36 LYS cc_start: 0.8768 (tppt) cc_final: 0.8517 (ttmm) REVERT: H 60 GLU cc_start: 0.8984 (mp0) cc_final: 0.8743 (mp0) REVERT: H 63 ARG cc_start: 0.8953 (ttm110) cc_final: 0.8653 (ttp-110) REVERT: H 68 GLN cc_start: 0.7844 (tm-30) cc_final: 0.7519 (tm-30) REVERT: H 81 ASP cc_start: 0.8573 (t0) cc_final: 0.8102 (m-30) REVERT: H 100 ASN cc_start: 0.8848 (p0) cc_final: 0.8614 (p0) REVERT: F 29 MET cc_start: 0.9102 (mpp) cc_final: 0.8860 (mpp) REVERT: F 53 ASP cc_start: 0.8876 (p0) cc_final: 0.8456 (p0) REVERT: F 103 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7512 (mp10) REVERT: J 495 ASP cc_start: 0.8225 (m-30) cc_final: 0.7999 (p0) REVERT: K 479 ASN cc_start: 0.8982 (t0) cc_final: 0.8683 (t0) REVERT: K 480 ASP cc_start: 0.9028 (t0) cc_final: 0.8737 (t0) REVERT: K 495 ASP cc_start: 0.8868 (t0) cc_final: 0.8488 (t0) REVERT: K 496 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8708 (m-80) REVERT: K 500 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8582 (tp30) REVERT: K 503 ASP cc_start: 0.9384 (p0) cc_final: 0.8876 (p0) outliers start: 103 outliers final: 64 residues processed: 617 average time/residue: 0.5991 time to fit residues: 419.5520 Evaluate side-chains 592 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 520 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 MET 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 479 ASN 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 123 LYS 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 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 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 R residue 2 VAL Chi-restraints excluded: chain R residue 28 ASP Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 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 109 MET Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain 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 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 28 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 79 HIS Chi-restraints excluded: chain F residue 103 GLN Chi-restraints excluded: chain F residue 114 LEU 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 496 PHE 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 65 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** 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 48 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 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** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 74 HIS Q 101 ASN S 48 ASN ** S 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 69 ASN H 101 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 102 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 = 0.3876 r_free = 0.3876 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.090434 restraints weight = 58382.933| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 4.98 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3519 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 : 0.757 12.463 27351 Z= 0.375 Chirality : 0.046 0.200 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.981 59.773 2719 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.64 % Allowed : 34.17 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.18), residues: 2415 helix: 1.85 (0.21), residues: 614 sheet: -0.12 (0.18), residues: 728 loop : 0.87 (0.23), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 63 TYR 0.028 0.002 TYR R 40 PHE 0.025 0.002 PHE D 15 TRP 0.003 0.000 TRP U 509 HIS 0.014 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00372 (20223) covalent geometry : angle 0.75655 (27351) hydrogen bonds : bond 0.03575 ( 892) hydrogen bonds : angle 4.89474 ( 2490) *********************** 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 643 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 543 time to evaluate : 0.792 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: 0.7605 (t0) cc_final: 0.7121 (OUTLIER) REVERT: A 88 ASP cc_start: 0.8512 (t0) cc_final: 0.8178 (t0) REVERT: A 123 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8642 (tptp) REVERT: A 132 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7394 (mtp85) REVERT: C 36 LYS cc_start: 0.8948 (tmmt) cc_final: 0.8597 (mmpt) REVERT: C 62 HIS cc_start: 0.8533 (t-90) cc_final: 0.8312 (t70) REVERT: C 63 ARG cc_start: 0.9382 (ptm160) cc_final: 0.9082 (ptm-80) REVERT: C 66 MET cc_start: 0.8934 (mmm) cc_final: 0.8674 (mmm) REVERT: D 17 ARG cc_start: 0.8964 (ppp80) cc_final: 0.8716 (ptm-80) REVERT: D 32 ARG cc_start: 0.8844 (mtm180) cc_final: 0.8235 (mtp180) REVERT: D 81 ASP cc_start: 0.8371 (m-30) cc_final: 0.7772 (m-30) REVERT: D 93 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 135 ASP cc_start: 0.8333 (m-30) cc_final: 0.7888 (m-30) REVERT: B 59 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8588 (mmmt) REVERT: B 63 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8903 (tmm-80) REVERT: B 101 ASN cc_start: 0.9256 (t0) cc_final: 0.8559 (t0) REVERT: B 109 MET cc_start: 0.7950 (mtt) cc_final: 0.7680 (mtt) REVERT: L 477 ASP cc_start: 0.8944 (p0) cc_final: 0.8737 (p0) REVERT: L 486 LEU cc_start: 0.8507 (tp) cc_final: 0.8189 (mp) REVERT: L 502 ASP cc_start: 0.7858 (m-30) cc_final: 0.7558 (t0) REVERT: I 479 ASN cc_start: 0.8862 (t0) cc_final: 0.8102 (t0) REVERT: I 480 ASP cc_start: 0.8819 (t0) cc_final: 0.7939 (p0) REVERT: I 495 ASP cc_start: 0.8564 (t70) cc_final: 0.8285 (t0) REVERT: I 497 LEU cc_start: 0.9120 (mm) cc_final: 0.8766 (pp) REVERT: P 88 ASP cc_start: 0.8407 (t0) cc_final: 0.7881 (t0) REVERT: P 102 ASN cc_start: 0.8806 (t0) cc_final: 0.8512 (t0) REVERT: P 123 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8367 (tptm) REVERT: N 1 MET cc_start: 0.7466 (tpp) cc_final: 0.6904 (tpp) REVERT: N 3 MET cc_start: 0.7049 (tpp) cc_final: 0.6666 (tpp) REVERT: N 29 MET cc_start: 0.8959 (tpt) cc_final: 0.8422 (tpt) REVERT: N 68 GLN cc_start: 0.8140 (mp10) cc_final: 0.7723 (mp10) REVERT: N 117 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8185 (tm-30) REVERT: N 123 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8048 (tppp) REVERT: M 17 ARG cc_start: 0.8998 (ppp80) cc_final: 0.8722 (ppp80) REVERT: M 32 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8586 (mmm-85) REVERT: M 63 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8221 (ttm110) REVERT: M 93 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8142 (tm-30) REVERT: M 103 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: O 59 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8533 (mmmt) REVERT: O 60 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8377 (mm-30) REVERT: O 63 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8449 (ttp80) REVERT: O 103 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: V 477 ASP cc_start: 0.8639 (p0) cc_final: 0.8408 (p0) REVERT: V 502 ASP cc_start: 0.8249 (m-30) cc_final: 0.7419 (p0) REVERT: U 479 ASN cc_start: 0.8564 (t0) cc_final: 0.8241 (t0) REVERT: U 496 PHE cc_start: 0.8717 (m-10) cc_final: 0.8368 (m-10) REVERT: U 500 GLU cc_start: 0.9013 (tt0) cc_final: 0.8661 (tp30) REVERT: T 76 LYS cc_start: 0.8340 (tptm) cc_final: 0.8102 (tptp) REVERT: T 88 ASP cc_start: 0.8127 (t0) cc_final: 0.7855 (t0) REVERT: R 37 ASN cc_start: 0.8388 (t160) cc_final: 0.8102 (m-40) REVERT: Q 14 GLU cc_start: 0.9317 (tp30) cc_final: 0.8846 (tp30) REVERT: Q 63 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8127 (ttm110) REVERT: Q 93 GLN cc_start: 0.8653 (pp30) cc_final: 0.7969 (pp30) REVERT: Q 123 LYS cc_start: 0.8718 (tptt) cc_final: 0.8511 (ttmt) REVERT: Q 134 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8090 (tm-30) REVERT: Q 136 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8680 (pp20) REVERT: S 63 ARG cc_start: 0.9201 (tmm-80) cc_final: 0.8938 (ttp80) REVERT: S 81 ASP cc_start: 0.8076 (t0) cc_final: 0.7814 (p0) REVERT: S 93 GLN cc_start: 0.8020 (tt0) cc_final: 0.7799 (tt0) REVERT: W 479 ASN cc_start: 0.8592 (t0) cc_final: 0.8305 (t0) REVERT: W 496 PHE cc_start: 0.8730 (m-80) cc_final: 0.8520 (m-10) REVERT: E 59 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8705 (mmmt) REVERT: E 76 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7597 (tptp) REVERT: E 109 MET cc_start: 0.9011 (ptm) cc_final: 0.8728 (ptp) REVERT: G 48 ASN cc_start: 0.9245 (t0) cc_final: 0.8958 (p0) REVERT: H 17 ARG cc_start: 0.8977 (ppp80) cc_final: 0.8609 (ppp80) REVERT: H 32 ARG cc_start: 0.9064 (mmm-85) cc_final: 0.8715 (mmm-85) REVERT: H 36 LYS cc_start: 0.8801 (tppt) cc_final: 0.8535 (ttmm) REVERT: H 60 GLU cc_start: 0.8952 (mp0) cc_final: 0.8649 (mm-30) REVERT: H 68 GLN cc_start: 0.7807 (tm-30) cc_final: 0.7553 (tm-30) REVERT: H 81 ASP cc_start: 0.8546 (t0) cc_final: 0.8068 (m-30) REVERT: H 106 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7956 (mtp180) REVERT: F 29 MET cc_start: 0.9080 (mpp) cc_final: 0.8813 (mpp) REVERT: F 53 ASP cc_start: 0.8870 (p0) cc_final: 0.8436 (p0) REVERT: F 103 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: J 495 ASP cc_start: 0.8221 (m-30) cc_final: 0.8004 (p0) REVERT: K 479 ASN cc_start: 0.8979 (t0) cc_final: 0.8677 (t0) REVERT: K 480 ASP cc_start: 0.9046 (t0) cc_final: 0.8771 (t0) REVERT: K 495 ASP cc_start: 0.8863 (t0) cc_final: 0.8469 (t0) REVERT: K 500 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8145 (tm-30) outliers start: 100 outliers final: 68 residues processed: 609 average time/residue: 0.6147 time to fit residues: 423.4331 Evaluate side-chains 604 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 528 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 109 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL 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 41 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 95 MET 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 479 ASN 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 123 LYS 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 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 T residue 94 VAL 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 99 SER 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 109 MET Chi-restraints excluded: chain Q residue 136 GLU Chi-restraints excluded: chain Q residue 137 VAL Chi-restraints excluded: chain S residue 80 VAL Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain 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 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 28 ASP 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 75 THR Chi-restraints excluded: chain G residue 103 GLN Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS Chi-restraints excluded: chain H residue 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 488 SER Chi-restraints excluded: chain K residue 485 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 227 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 224 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 95 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** 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 128 ASN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN Q 18 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 62 HIS S 68 GLN ** 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** G 128 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.117113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092331 restraints weight = 72946.138| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 5.57 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20223 Z= 0.144 Angle : 0.783 12.809 27351 Z= 0.385 Chirality : 0.046 0.197 2905 Planarity : 0.004 0.053 3638 Dihedral : 4.896 59.475 2715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.34 % Allowed : 35.56 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.18), residues: 2415 helix: 1.77 (0.21), residues: 614 sheet: -0.06 (0.18), residues: 728 loop : 0.91 (0.23), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 63 TYR 0.018 0.001 TYR S 125 PHE 0.023 0.002 PHE D 15 TRP 0.003 0.000 TRP W 509 HIS 0.013 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00337 (20223) covalent geometry : angle 0.78297 (27351) hydrogen bonds : bond 0.03449 ( 892) hydrogen bonds : angle 4.89671 ( 2490) ********************** 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 632 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 560 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.9097 (m-30) cc_final: 0.8647 (p0) REVERT: A 81 ASP cc_start: 0.7599 (t0) cc_final: 0.7162 (t0) REVERT: A 88 ASP cc_start: 0.8527 (t0) cc_final: 0.8203 (t0) REVERT: A 123 LYS cc_start: 0.9169 (mmmt) cc_final: 0.8646 (tptp) REVERT: A 132 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7177 (mtp85) REVERT: C 32 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8033 (mtp-110) REVERT: C 36 LYS cc_start: 0.8913 (tmmt) cc_final: 0.8596 (mmpt) REVERT: C 62 HIS cc_start: 0.8481 (t-90) cc_final: 0.8249 (t70) REVERT: C 63 ARG cc_start: 0.9387 (ptm160) cc_final: 0.9080 (ptm-80) REVERT: C 66 MET cc_start: 0.8945 (mmm) cc_final: 0.8671 (mmm) REVERT: D 17 ARG cc_start: 0.8934 (ppp80) cc_final: 0.8683 (ptm-80) REVERT: D 32 ARG cc_start: 0.8847 (mtm180) cc_final: 0.8272 (mtp180) REVERT: D 81 ASP cc_start: 0.8381 (m-30) cc_final: 0.7638 (m-30) REVERT: D 93 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7581 (tm-30) REVERT: D 135 ASP cc_start: 0.8344 (m-30) cc_final: 0.7898 (m-30) REVERT: B 59 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8586 (mmmt) REVERT: B 63 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8921 (tmm-80) REVERT: B 101 ASN cc_start: 0.9196 (t0) cc_final: 0.8509 (t0) REVERT: B 109 MET cc_start: 0.7771 (mtt) cc_final: 0.7532 (mtt) REVERT: L 477 ASP cc_start: 0.8926 (p0) cc_final: 0.8722 (p0) REVERT: L 486 LEU cc_start: 0.8506 (tp) cc_final: 0.8178 (mp) REVERT: L 502 ASP cc_start: 0.7837 (m-30) cc_final: 0.7530 (t0) REVERT: I 479 ASN cc_start: 0.8839 (t0) cc_final: 0.8084 (t0) REVERT: I 480 ASP cc_start: 0.8764 (t0) cc_final: 0.7876 (p0) REVERT: I 484 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8481 (mm-30) REVERT: I 497 LEU cc_start: 0.9165 (mm) cc_final: 0.8791 (pp) REVERT: P 88 ASP cc_start: 0.8364 (t0) cc_final: 0.7826 (t0) REVERT: P 102 ASN cc_start: 0.8795 (t0) cc_final: 0.8480 (t0) REVERT: P 123 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8258 (tptm) REVERT: N 1 MET cc_start: 0.7533 (tpp) cc_final: 0.6915 (tpp) REVERT: N 3 MET cc_start: 0.6914 (tpp) cc_final: 0.6528 (tpp) REVERT: N 29 MET cc_start: 0.8949 (tpt) cc_final: 0.8390 (tpt) REVERT: N 36 LYS cc_start: 0.8656 (tmmt) cc_final: 0.8258 (mppt) REVERT: N 68 GLN cc_start: 0.8151 (mp10) cc_final: 0.7694 (mp10) REVERT: N 107 ARG cc_start: 0.7409 (mmt90) cc_final: 0.6941 (mmt90) REVERT: N 117 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8192 (tm-30) REVERT: N 123 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8052 (tppp) REVERT: M 17 ARG cc_start: 0.9019 (ppp80) cc_final: 0.8730 (ppp80) REVERT: M 25 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: M 32 ARG cc_start: 0.9020 (mmm-85) cc_final: 0.8598 (mmm-85) REVERT: M 63 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8326 (ttm110) REVERT: M 93 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8145 (tm-30) REVERT: M 103 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: O 60 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8366 (mm-30) REVERT: O 63 ARG cc_start: 0.9111 (ttt-90) cc_final: 0.8451 (ttp80) REVERT: O 103 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: V 477 ASP cc_start: 0.8603 (p0) cc_final: 0.8335 (p0) REVERT: V 502 ASP cc_start: 0.8223 (m-30) cc_final: 0.7441 (p0) REVERT: U 479 ASN cc_start: 0.8587 (t0) cc_final: 0.8277 (t0) REVERT: U 496 PHE cc_start: 0.8683 (m-10) cc_final: 0.8279 (m-10) REVERT: U 500 GLU cc_start: 0.9042 (tt0) cc_final: 0.8664 (tp30) REVERT: T 32 ARG cc_start: 0.8488 (mtp85) cc_final: 0.7780 (mtp180) REVERT: T 76 LYS cc_start: 0.8306 (tptm) cc_final: 0.8096 (tptp) REVERT: T 88 ASP cc_start: 0.8107 (t0) cc_final: 0.7810 (t0) REVERT: R 29 MET cc_start: 0.8980 (tpt) cc_final: 0.8425 (tpt) REVERT: Q 14 GLU cc_start: 0.9317 (tp30) cc_final: 0.8845 (tp30) REVERT: Q 32 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8739 (mmm-85) REVERT: Q 63 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8205 (ttm110) REVERT: Q 93 GLN cc_start: 0.8612 (pp30) cc_final: 0.7843 (pp30) REVERT: Q 123 LYS cc_start: 0.8719 (tptt) cc_final: 0.8506 (ttmt) REVERT: Q 136 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8684 (pp20) REVERT: S 63 ARG cc_start: 0.9226 (tmm-80) cc_final: 0.8955 (ttp80) REVERT: S 93 GLN cc_start: 0.7941 (tt0) cc_final: 0.7300 (tt0) REVERT: X 500 GLU cc_start: 0.8052 (tt0) cc_final: 0.7659 (tt0) REVERT: W 479 ASN cc_start: 0.8590 (t0) cc_final: 0.8308 (t0) REVERT: W 496 PHE cc_start: 0.8612 (m-80) cc_final: 0.8167 (m-10) REVERT: E 14 GLU cc_start: 0.8551 (tp30) cc_final: 0.8323 (tp30) REVERT: E 59 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8731 (mmtt) REVERT: E 76 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7901 (tptp) REVERT: E 109 MET cc_start: 0.9037 (ptm) cc_final: 0.8835 (ptp) REVERT: G 48 ASN cc_start: 0.9256 (t0) cc_final: 0.9002 (p0) REVERT: H 17 ARG cc_start: 0.8945 (ppp80) cc_final: 0.8585 (ppp80) REVERT: H 32 ARG cc_start: 0.9052 (mmm-85) cc_final: 0.8725 (mmm-85) REVERT: H 36 LYS cc_start: 0.8777 (tppt) cc_final: 0.8492 (ttmm) REVERT: H 60 GLU cc_start: 0.8951 (mp0) cc_final: 0.8613 (mm-30) REVERT: H 63 ARG cc_start: 0.8930 (ttm110) cc_final: 0.8220 (ttm110) REVERT: H 68 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7359 (tm-30) REVERT: H 69 ASN cc_start: 0.7603 (t0) cc_final: 0.7033 (m-40) REVERT: H 81 ASP cc_start: 0.8546 (t0) cc_final: 0.8082 (m-30) REVERT: H 100 ASN cc_start: 0.8809 (p0) cc_final: 0.8536 (p0) REVERT: F 29 MET cc_start: 0.9088 (mpp) cc_final: 0.8838 (mpp) REVERT: F 53 ASP cc_start: 0.8869 (p0) cc_final: 0.8469 (p0) REVERT: F 103 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: J 495 ASP cc_start: 0.8201 (m-30) cc_final: 0.7984 (p0) REVERT: K 479 ASN cc_start: 0.8976 (t0) cc_final: 0.8678 (t0) REVERT: K 480 ASP cc_start: 0.9040 (t0) cc_final: 0.8760 (t0) REVERT: K 495 ASP cc_start: 0.8845 (t0) cc_final: 0.8439 (t0) REVERT: K 500 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8066 (tm-30) outliers start: 72 outliers final: 56 residues processed: 614 average time/residue: 0.5910 time to fit residues: 412.4427 Evaluate side-chains 587 residues out of total 2155 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 522 time to evaluate : 0.787 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 95 MET 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 479 ASN Chi-restraints excluded: chain I residue 473 ILE Chi-restraints excluded: chain I residue 474 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 123 LYS Chi-restraints excluded: chain P residue 137 VAL Chi-restraints excluded: chain N residue 55 VAL 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 492 THR Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain Q residue 41 VAL 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 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 137 VAL Chi-restraints excluded: chain X 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 H residue 41 VAL Chi-restraints excluded: chain H residue 73 CYS 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 K residue 485 SER Chi-restraints excluded: chain K residue 500 GLU Chi-restraints excluded: chain K residue 503 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 135 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 73 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS A 103 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN D 101 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 GLN ** P 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN Q 18 GLN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 101 ASN S 48 ASN ** 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** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS F 62 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.091423 restraints weight = 64201.023| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 5.24 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3694 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= 0.156 Angle : 0.779 11.870 27351 Z= 0.386 Chirality : 0.046 0.200 2905 Planarity : 0.004 0.052 3638 Dihedral : 4.918 59.242 2715 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.99 % Allowed : 35.65 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.18), residues: 2415 helix: 1.77 (0.21), residues: 614 sheet: -0.01 (0.18), residues: 712 loop : 0.86 (0.22), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 63 TYR 0.028 0.002 TYR G 40 PHE 0.024 0.002 PHE H 15 TRP 0.002 0.000 TRP U 509 HIS 0.015 0.001 HIS F 79 Details of bonding type rmsd covalent geometry : bond 0.00367 (20223) covalent geometry : angle 0.77878 (27351) hydrogen bonds : bond 0.03539 ( 892) hydrogen bonds : angle 4.88171 ( 2490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8282.11 seconds wall clock time: 142 minutes 15.11 seconds (8535.11 seconds total)